Macs in Chemistry

Insanely Great Science

computational chemistry

IM-UFF: extending the Universal Force Field for interactive molecular modeling

 

An interesting development for those working in nano materials.

We have completed the development of IM-UFF (Interactive Modeling - UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physically-based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience.

This contribution has been submitted to the Journal of Molecular Modeling.

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON’s generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means “Software for Adaptive Modeling and Simulation Of Nanosystems”.

macLaunch


Comments

Grand Challenge 3

 

I've written a couple of docking/virtual screening workflows using SMINA, a freely available tool DOI. There are a number of other alternatives and it is very difficult to get good comparisons which is why the Grand Challenges are useful.

The Grand Challenge 3 (GC3) is a blinded prediction challenge for the computational chemistry community, with components addressing pose-prediction, affinity ranking, and free energy calculations. GC3 is based on six different protein targets, Cathepsin S and five different kinases, and is separated into five subchallenges, some of which involve multiple protein targets. Only Cathepsin S is associated with cocrystal structures, so the kinase components of this challenge focus on affinity ranking and/or free energy predictions. Three of the datasets, Cathepsin S, JAK2 and TIE2, include a free energy prediction component.

This is an ideal opportunity to test novel algorithms on a carefully curated dataset.

Computational practices often employ a number of computational algorithms and dataset preparation steps for meaningful results. D3R will provide a forum for deposition, dissemination and discussion of such workflows through this website. Workflows will represent methods used successfully in the blinded challenges and methods donated by our pharmaceutical and/or academic collaborators. GitHub.

In Stage 1 September 1 - October 1, your predicted poses for the 24 ligands, in a coordinate system aligned with the S04-bound Cathepsin S structure provided in the inputs. Your predicted affinities, or affinity rankings, for all 136 compounds and/or your predicted absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds. When Stage 1 closes, we will release the crystallographic poses of the 24 ligands.

In Stage 2 October 1 - December 1, your predictions of the affinity rankings of all 136 compounds and/or absolute or relative binding affinities (in kcal/mol) for the free energy subset of 33 compounds.

Full details and registration.

Comments

Facio GUI for CompChem

 

Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).

Current Version of Facio : 20.1.2 (released on August 17 2017) for Mac (Mac OS X10.6 or later and macOS Sierra)

Pasted Graphic


Comments

Gabedit 2.5.0 released

 

The new version (2.5.0) of Gabedit has been released and is available for download at http://gabedit.sourceforge.net/

Gabedit is a graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and Q-Chem. It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.

Here is a list of the significant changes between 2.5.0 and 2.4.8:

  • Minor bugs fixed.
  • New tools for VASP :

    • read geometries (Optimization or M. Dynamic) from VASP OUTCAR file
    • read geometry from VASP POSCAR file
    • Create VASP POSCAR file
    • Read dielectric function from a VASP xml file and compute optic properties : the refractive index n(w), the extinction coefficient k(w), the absorption coefficient alpha(w), the reflectivity R(w), the energy loss spectrum L(w), and the optical conductivity sigma(w).

      • read data from vasprun.xml and plot DOS, pDOS and, Bands structures
  • Gabedit can now read the hessian from .hess orca file. After reading of the hessian, Gabedit computes frequencies, modes and effective masses.
  • Export in CChemI : update
  • Tv accepted (used by Gaussian and Mopac for periodic system). Using Tv, Gabedit can generate other cells.
  • deMon2k is now supported (Thanks to Dennis Salahub, Mauricio Chagas da Silva, Jonathan Kung and Morteza Chehelamirani for their suggestions, corrections, comments,...)
  • Gabedit can now compute the anharmonic spectrum by QM/MMFF94 method using iGVPT2 program. Gabedit can read the harmonic and anharmonic spectra from an iGVPT2 output file.
  • Energy, geometry optimization, MD, MD Conformations search by MMFF94, MMFF94s, UFF and Ghemical potentials are now supported by Gabedit via Open Babel.
  • Energy, geometry optimization, MD, MD Conformations search using your own program (potential) are now supported. DFTB+ is supported via this new tool.

Instructions for compiling under Mac OSX are here https://sites.google.com/site/allouchear/Home/gabedit/download/compilation-under-macosx.


Comments

Schrödinger Updated

 

The Schrödinger small molecule discovery suite has ben updated. This looks to be a substantial update and is described in the video below.

Supported MacOS X 10.12 and Mac OS X 10.9 - 10.11

3D Support, Supported: Interlaced stereo via Zalman 3D Monitors


Comments

CRYSTAL14 v1.0.4 released

 

Crystal14 Version 1.0.4 is mainly a bugfix release. All users are encouraged to upgrade to v1.0.4 as soon as possible.

This is the list of options which have been fixed in the v1.0.4 version of CRYSTAL14:

  • Electronic band structure for open-shell systems (asymmetric k-points only)
  • Piezoelectricity of 1D and 2D cases (non-periodic directions fixed)
  • Piezoelectricity for open-shell systems
  • BREAKELAST option restored
  • ATOMINSE+SUPERCELL combination fixed
  • Cell gradients for charged systems
  • Range-separated hybrids (conflict with bipolar approximation fixed)
  • Some static limits for CLUSTER option have been relaxed
  • Small fixes (normalization, k-points coordinates) in phonon bands and density-of-states
  • CUBE format for 3D plots of charge density and electrostatic potential fixed
  • Various fixes in restart options of vibration frequencies + IR and Raman intensities calculation
  • HJS exchange hole for open shell systems. This affects HSE06, HSEsol, HISS, LC-wPBE, LC-wPBEsol and LC-wBLYP functionals.
  • Fixes in the POTC option

Comments

Psi4 1.1: An Open-Source Electronic Structure Program

 

A recent paper describes Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability DOI

Psi4 is an ab initio electronic structure program providing methods such as Hartree–Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools.

Psi4 1.1 can be downloaded from here with versions supporting Python 2.7, 3.5 and 3.6.

Note the installation instructions for Mac: Install XCode via the App Store, Make sure you open XCode and accept the license agreement after you install.


Comments

Conformer generation

 

The generation of multiple conformations is an important step in a number of operations from input to ab initio calculations to providing input files for docking studies. A recent paper compared seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK DOI, and also provided a dataset of ligand conformations taken from the PDB.

A recent twitter discussion involving Greg Landrum and David Koes prompted Greg to publish a blog post describing conformation generation within RDKit. The post compares using distance geometry to select diverse conformations versus an approach that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data (ETKDG). He also looks at the impact of force-field minimisation.

A really interesting read with code provided.


Comments

ADF Modeling Suite 2017

 

Just looking at the release notes for ADF2017 and support pages and a couple of things caught my eye.

The python distribution shipped with ADF was upgraded to python 3.5. Among others, new and updated modules include the iPython interpreter for easier development of python codes, a number of useful packages such as numpy 1.11.3 / scipy 0.18.1, ASE 3.13.0, matplotlib and RDKit 2016.09.

The Mac OSX version no longer requires XQuartz and is much faster in visualizing large systems.


Comments

ADF Modeling Suite 2017

 

I just got this message

We are proud to announce the 2017 release of the ADF Modeling Suite, with excellent contributions from our collaborators and the continued efforts of the SCM team in Amsterdam.

Exciting new features include
Spectroscopy-

  • Many new NLO properties (TPA, THG, ...): Hu, Autschbach & Jensen
  • Constrained DFT with excited states: Ramos & Pavanello
  • LFDFT for d-d and d-f transitions: Ramanantoanina & Daul
  • CV-DFT for singlet-triplet excitations: Krykunov, Senn, Park & Seidu
  • Faster periodic response with TD(C)DFT, including 2D systems: Raupach
  • VCD analysis tools: Nicu

Reactivity & Analysis-

  • Latest xc functionals (SCAN, MN15-L, ....): interface to libxc 3.0
  • Special points, fat bands and improved pDOS analysis
  • GUI support for NEGF with BAND (Thijssen group, includes self-consistent NEGF, gate & bias potential, spin transport) and post-SCF DFTB-NEGF (Heine group)
  • FDE + local COSMO: Goez & Neugebauer
  • Reactivity descriptors from conceptual DFT and QTAIM: Tognetti & Joubert
  • Geometry optimization with SpinFlip in QUILD: Swart
  • Spin-polarization and l-dependency for DFTB: Melix, Oliveira, Rueger, Heine
  • Much faster periodic DFTB(+D) optimizations, latest DFTB.org parameters freely available
  • eReaxFF including explicit electrons: based on Islam, Verstraelen & van Duin
  • Controllable mass-scaling for force bias Monte Carlo ReaxFF: Bal & Neyts
  • Improved VLE, LLE, IDAC, kOW with reparameterized COSMO-SAC: Chen & Lin

GUI & Builders-

  • Quantum ESPRESSO: GUI interface & binaries
  • MOF builder and UFF4MOFsII: Coupry, Addicoat, Heine
  • Much faster visualization of large and periodic systems
  • Set up and visualize 'molecule gun' calculations with ReaxFF

For a more comprehensive list and details see: www.scm.com/support/release-notes


Comments

ORCA 4.0 released

 

The latest update to ORCA has just been released.

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

New Features of Version 4.0:

New Methods:

  • Linear scaling DLPNO-CCSD(T) open shell. New restricted open-shell formulation
  • Linear scaling DLPNO-MP2 (RHF and UHF)
  • Linear scaling DLPNO-MP2-F12 (RHF)
  • Linear scaling DLPNO-CCSD(T) (the 2013 implementation is still available)
  • Linear scaling DLPNO-CCSD(T) local energy decomposition scheme
  • Linear scaling DLPNO-CCSD closed shell density
  • Linear scaling cluster in molecule (CIM): MP2, CCSD(T), DLPNO-CCSD(T)
  • Linear scaling DLPNO-NEVPT2
  • NEVPT2-F12
  • Updated interface to BLOCK 1.0
  • DMRG-NEVPT2
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Partial PNO-EOM-CCSD method for excited states
  • Partial PNO-STEOM-CCSD method for excited states
  • DLPNO-CCSD-F12, LPNO-CCSD-F12
  • Mukherjee Mk-LPNO-MRCCSD(T)
  • Powerful iterative configuration expansion (ICE-CI) approximation to Full-CI
  • ICE-CI for large active space CASSCF calculations
  • MREOM-CCSD (also with SOC)
  • Fully internally contracted MRCI
  • Full TD-DFT energies and gradient for hybrid functionals
  • Super-fast approximate TD-DFT: sTDA/sTDDFT of Grimme and co-workers
  • PBEh-3c method of Grimme and co-workers

SCF, DFT and Hessian:

  • Large performance improvements for calculations with four center integrals
  • Improved performance with RI-J with conventionally stored integrals
  • Gradient for range separated hybrids
  • Gradient for range double hybrid functionals with meta GGAs
  • Gradient for range double hybrid functionals with range separated functionals
  • Gradient for RI-JK
  • Frequencies for range separated functionals
  • Stability analysis and automatic search for broken symmetry states
  • Local spin analysis
  • Fractional occupation number analysis (FOD) for detection of MR character

MDCI module:

  • All improvements for DLPNO methods as listed above
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Automatic closed shell STEOM-CCSD active space selection
  • EOM-CCSD(2) and STEOM-CCSD(2) approximations
  • EOM-CCSD transition moments
  • EOM/STEOM-CCSD core level excited states
  • IP-EOM-CCSD and EA-EOM-CCSD
  • ADC(2) and CC(2) methods (initial implementation)
  • COSX for EOM-CCSD and STEOM-CCSD
  • Improved automatic frozen core handling
  • Core-correlation in automatic basis set extrapolation

AUTOCI module:

  • RHF/UHF CISD
  • RHF/UHF CCSD
  • ROHF CISD
  • ROHF CCSD
  • FIC-MRCI, CEPA/0 variant and DDCI3

CASSCF, NEVPT2 and MRCI

  • Detailed tutorial showing CASSCF/NEVPT2 usage
  • Accelerated CI (ACCCI) a more efficient CI step for multi-root calculations
  • Automatic implementation of AbInitio ligand-field theory
  • Simplified generation of double-shell orbitals
  • Active space protection scheme and improved warnings
  • ICE-CI as CI solver for larger active spaces
  • Partially Contracted NEVPT2 with and without RI
  • Updated interface to BLOCK 1.0
  • DMRG-NEVPT2 for active spaces up to 20 orbitals
  • Magnetization and magnetic susceptibility
  • Printing of the wavefunction in terms of CSFs and spin-determinants
  • MREOM-CCSD (also with SOC)
  • Local spin analysis for CASSCF
  • Fragment decomposition of the spin-spin interaction
  • Cumulant approximation for NEVPT2
  • ACCCI as CIStep for FIC and DLPNO-NEVPT2
  • Explicitly correlated RI-FIC-NEVPT2 (NEVPT2-F12)

TD-DFT and ROCIS:

  • Full TD-DFT for hybrid functionals
  • Gradient for full TD-DFT with hybrid functionals
  • TD-DFT/TDA gradient with range separated functionals
  • ROCIS magnetic properties (hyperfine, g-tensor, ZFS tensor, MCD)
  • ROCIS-RIXS spectra
  • PNO-ROCIS for spectacular performance improvements
  • Super-fast approximate TD-DFT: sTDA/sTDDFT
  • Natural transition orbitals in TD-DFT and ROCIS

Miscellaneous:

  • GIAO implementation for NMR chemical shifts. Various aproximations (RIJOCOSX, RIJK)
  • New Handling of basis set names. Now fully consistent with TurboMole def2-defaults (including ECPs) SARC basis sets separately available
  • New reading of basis sets and ECPs together
  • New correlation consistent basis sets added
  • New SARC basis sets for the lanthanides; good for correlated calculations
  • New ANO-RCC basis sets added
  • Improved frozen core handling in correlation calculations
  • Improved automatic auxiliary basis set generation
  • Corrections for low-frequency modes in thermochemistry
  • New and improved NBO interface
  • CPCM and improved SMD solvent models
  • Intrinsic atomic orbital (IAO) and bond orbital implementation
  • Improved performance in Boys localization
  • Updated and improved mapspc program
  • Atomic Mean Field (AMFI) spin-orbit coupling operators
  • EPRNMR works with range separated hybrid functionals
  • New molecular dynamics module

Comments

Conformation generation

 

Most drug-like molecules contain a number of rotatable bonds and prediction of bioactivities, docking etc. require an understanding of conformation. Whilst systematic methods can in theory explore all conformational space, however as the number of rotatable bonds increases a systematic search becomes prohibitive both in terms of the computational cost in generating conformations but also the time taken to process all the generated conformations (e.g. dock into protein). Thus there is great interest in rapid means to generate ensembles of representative conformations.

confs

A recent paper DOI helps to address the problem by compiling a high quality dataset of structures generated using ligands from the Protein Data Bank.

The datasets were applied to benchmarking seven freely available conformer ensemble generators: Balloon (two different algorithms), the RDKit standard conformer ensemble generator, the Experimental-Torsion basic Knowledge Distance Geometry (ETKDG) algorithm, Confab, Frog2 and Multiconf-DOCK. Substantial differences in the performance of the individual algorithms were observed, with RDKit and ETKDG generally achieving a favorable balance of accuracy, ensemble size and runtime.

The dataset is freely available for download http://www.zbh.uni-hamburg.de/?id=628


Comments

MOE updated

 

Chemical Computing Group have announced and update to MOE. The MOE 2016.0802 update contains a number of updates to the biomolecule modelling including improved hydrogen bond detection, and addition of a number of unnatural amino acids.

There have also been improvements to MOE/Web MOE/web. The MOE/web version compatibility check has been broadened. MOE/web license waiting has been improved. HTTPS authentication proxy server support has been improved.


Comments

Tinker Updated

 

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....

TINKER 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means TINKER can now support very large molecular systems. TINKER 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous TINKER version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of TINKER. In particular, older versions of parameter files should not be used with TINKER 8 executables and vice versa.


Comments

Publishing computational notebooks with Binder

 

I've now written a couple of Jupyter notebooks and one of the issues that has come up is how to share the notebooks in a way that ensures the results will be reproducible in an environment when updates to components occur regularly.

Binder is a collection of tools for building and executing version-controlled computational environments that contain code, data, and interactive front ends, like Jupyter notebooks. It's 100% open source.

At a high level, Binder is designed to make the following workflow as easy as possible

  • Users specify a GitHub repository
  • Repository contents are used to build Docker images
  • Deploy containers on-demand in the browser on a cluster running Kubernetes

Common use cases include:

  • sharing scientific work
  • sharing journalism
  • running tutorials and demos with minimal setup
  • teaching courses

binder

If you want to find out more have a look at this blog post by the developers.


Comments

Maestro 11 training

 

A nice image from the Maestro 11 training session run by Schrödinger, it looks like there are a few more training sessions coming up also.

maestro11

Maestro 11 is the portal to all of Schrödinger's computational technology – far more than just a user interface, Maestro 11 also helps researchers organize and analyze data.


Comments

Added PUPIL to alphabetical listing

 

PUPIL,Program for User Package Interface and Linking, is a software environment - the program - that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be implemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.


Comments

ICM version 3.8-5

 

MolSoft have announced the release of ICM version 3.8-5.

  • Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
  • 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
  • ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
  • Support for MMTF format. The Macromolecular Transmission Format (MMTF)
  • Support for Mac retina display
  • Add docking restraints by selecting atoms in the receptor
  • Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here


Comments

MOE 2016.08 released

 

Chemical Computing Group have just announced an update to MOE. This release has fixed a couple of Mac OSX 10.12 (Sierra) issues but also brings a host of new features.

  • MOEsaic: Web-Application for Ligand Analytics
  • Spectral Analysis for Structure Determination
  • Enhanced Protein Patch Analyzer
  • Integrated Antibody Project Database and Antibody Homology Modeler
  • Small Footprint MOE to Facilitate Large Scale Deployments
  • Physical and Virtual Rendering of Structures

A more detailed description of the new and enhanced features in MOE 2016.08 can be found at http://www.chemcomp.com/print/moe2016.08.pdf.


Comments

APBS 1.5 released

 

The latest version of APBS includes several notable features and bug fixes. This release includes the addition of Poisson-Boltzmann Analytical-Method (PB-AM), Poisson-Boltzmann Semi-Analytical Method (PB-SAM) and the Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI). Additionally, we have made improvements to the build system and the system tests, as well as miscellaneous bug fixes.

APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules. Solve the Poisson-Boltzmann and related equations to calculate solvation energies and electrostatic properties for analysis and visualization

APBS 1.5 changes

Binary releases may be found on GitHub and on SourceForge. New Features

  • Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS.
  • PBSAM is currently only available in the Linux and OS X distributions.
  • Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
  • More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
  • Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
  • Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
  • Included NanoShaper alternative to MSMS.
  • More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
  • Added binary DX format support to the appropriate APBS tools.
  • Test suite amended and expanded.
  • Removed hard-coded limitation to number of grid points used to determine surface accessibility.

Known Bugs / Limitations

  • PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

Full details here


Comments

QUACPAC v1.7.0 released

 

Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage.

This update contains amount other things

  • Significant improvements have been made to the reasonable tautomer algorithm that affect its aliphatic and non-aromatic resonance portions.
  • Inclusion of AM1BCC ELF10, a new method for applying partial charges to a molecule
  • TIP3P water charges are now assigned when using Amber charge sets on molecules containing waters.

Support for Mac OS X 10.10 and 10.11 has been added.
Mac OS X 10.7 and 10.8 are no longer supported.

Full release notes are here


Comments

BioExcel: An Introduction

 

An overview of the BioExcel Project.

BioExcel is based on improving three aspects of biomolecular research. Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS (www.gromacs.org), HADDOCK (www.haddocking.org) and CPMD (www.cpmd.org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced. It’s also important to improve how easy it is for users to access and use these types of software. Not all researchers have experience in efficiently handling data and software. BioExcel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research. In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.


Comments

Facio

 

Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).

cubemo_w_m


Comments

GPView Wave Function Analysis and Visualization

 

The GPView program is a C++ package for wave function analysis and visualization.

It is developed and maintained by Tian Shi and Ping Wang Ref](http://arxiv.org/abs/1602.07302)

In this manuscript, we will introduce a recently developed program GPView, which can be used for wave function analysis and visualization. The wave function analysis module can calculate and generate 3D cubes for various types of molecular orbitals and electron density related with electronic excited states, such as natural orbitals, natural transition orbitals, natural difference orbitals, hole-particle density, detachment-attachment density and transition density. The visualization module of GPView can display molecular and electronic (iso-surfaces) structures. It is also able to animate single trajectories of molecular dynamics and non-adiabatic excited state molecular dynamics using the data stored in existing files. There are also other utilities help to extract and process the output of quantum chemistry calculations. The GPView provides full graphic user interface (GUI) which makes it very easy to use.

22


Comments

Amber16 and AmberTools16 released

 

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers

The Amber16 package builds on AmberTools16 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. Major new features include:

Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
Gaussian Accelerated Molecular Dynamics (CPU, GPU)
Support for external electric fields (CPU)
Expanded umbrella sampling support (GPU)
Constant pH supported with replica exchange along pH coordinate (GPU)
Support for gas phase MD (igb=6) (CPU, GPU)
Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.


Comments

PDB2PQR 2.1 released

 

A new version of PDB2PQR has been released.

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems

  • Added alternate method to do visualization using 3dmol.
  • Replaced the Monte Carlo method for generating titration curves with graph cut. See http://arxiv.org/abs/1507.07021 (If you prefer the Monte Carlo method, please use http://nbcr-222.ucsd.edu/pdb2pqr_2.0.0/)
  • Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
  • Added a check before calculating pKa's for large interactions energies.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. DOI

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. DOI


Comments

ADF Modeling Suite 2016

 

The ADF modelling suite has been a popular modelling package used in many areas of chemistry and materials science. SCM have recently announced an important update to ADF

Software for Chemistry & Materials (SCM) is an Amsterdam-based computational chemistry software company. Originally spinning out from the Vrije Universiteit as Scientific Computing & Modelling NV in 1995, the SCM team supports and develops the ADF Modeling Suite, centered around the flagship program Amsterdam Density Functional (ADF), which was originally developed in the 1970s in the theoretical chemistry department.

Key new features::

  • New XC functionals: range-separated hybrid HSE06, long-range corrected hybrids and new meta-GGAs
  • SM12 solvation model and Constrained DFT in ADF
  • Spectroscopy: excitations from CV(n)-DFT, fast TDDFT+TB and sTDDFT, X-ray emission, surface-enhanced ROA, new kernel for periodic TDDFT, vibrationally resolved spectra from TDDFTB, hole states in BAND
  • Improved robustness for SCC-DFTB, COSMO, periodic optimizations, new HF exchange scheme
  • Analysis: unrestricted and periodic energy decomposition (pEDA), Fukui functions, Natural Transition Orbitals
  • Reactivity, PES: Automated reaction pathways for ReaxFF trajectories, new Transition State search options, MECP, analytic lattice gradients
  • GUI: job chaining, multiple spectra, orbital interaction visualization
  • Scripting: ASE interface for all codes, scripting support for COSMO-RS, job chaining, extensions to FlexMD multi-scale dynamics
  • Parameters, databases: Quasinano15 including repulsive potentials for light elements, latest 3OB parameters, new parameter sets for ReaxFF, ionic liquids database COSMO-RS

Full release notes are here


Comments

iSpartan

 

iSpartan has been updated.

What's New in Version 1.4.6 Improved stability for iOS9 for Spartan'14 Parallel Suite (Serve)r users Enhanced charge labels in Sketch mode Increased electrostatic potential surfaces integrity

iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. The app allows any chemist fast and easy access to computational methods that have proven reliable for a large range of molecules.

ispartan


Comments

OpenEye Toolkit Updated

 

OpenEye have announced the release of OpenEye Toolkits v2016.Feb. These libraries include the usual support for C++, Python, C# and Java.

The update address several key features.

Security

OpenEye toolkits are used in web services that require protection from malicious users. The most obvious attack vector against the OpenEye toolkits is file format parsing since scientific file formats are complex and often underdefined and there is the potential for embedded malicious code. This update closes a number of potential vulnerabilities.

FastROCS TK: Database Loading Performance

An interesting development is that physical memory limits on GPU's mean that for loading larger libraries the loading of the dataset actually takes longer than the actual search. This release addresses that issue.

OEMedChem TK

This also contains first official release of OEMedChem TK, in particular access to matched molecular pairs.

This 2016.Feb release no longer support OSX 10.8 , but support has been added for OSX 10.11. This 2016.Feb release supports Python 3.5 for the following platforms: OSX 10.10, OSX 10.11, Ubuntu 12, Ubuntu 14, RedHat 6, and RedHat 7

Full release notes are here ….


Comments

NCIPLOT

 

Added NCIPLOT to the alphabetical listing of applications. NCI (Non-Covalent Interactions) is a visualization index based on the density and its derivatives. It enables identification of non-covalent interactions. NCIPLOT is available for download.

Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

NCIPLOT

Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.


Comments

WEBMO VERSION 16 RELEASED

 

WebMO version 16

WebMO version 16 has been officially released and is available for FREE download at http://www.webmo.net/download

New features in WebMO version 16 include:

  • Support for both iOS and Android WebMO free apps
  • Support for the newest versions of ORCA, PSI, and Q-Chem
  • Support for hydrogen bonds in the WebMO editor
  • Improved support for building/cleanup of fused aromatic rings
  • Incorporation of modern HTML5 user interface elements including: drag-and-drop of jobs between folders, fewer pop-up windows, live updating of output files while jobs run, and expandable results page
  • Support for unlimited number of user folders and sub-folders (Pro)
  • Enhanced support for resource specification with external batch queues (Enterprise)
  • Various bug fixes

Important changes in the previous version include:

  • Java security warnings are reduced/eliminated with new signed applet
  • Support for the newest versions of GAMESS, MOPAC
  • Lookup feature to build structures by name (type "aspirin" or "vancomycin")
  • Links to external databases to lookup molecular properties, spectra, and data
  • Huckel molecular orbital calculations from within Build Molecule page (Pro)

WebMO is the most popular interface to computational chemistry programs, with over 22,000 unique WebMO licenses issued to date!

WEBMO iOS AND ANDROID APPS

WebMO has released a new Android app and updated its popular Apple iOS app!

The WebMO apps for portable devices are FREE.  

The Android and iOS WebMO apps provide equivalent features including:

  • Standalone molecular editing, optimization, symmetry, and orbital calculations
  • Integrated web lookup of molecular properties, spectra, and data
  • Access to WebMO servers (Free, Pro, and Enterprise versions of WebMO 16 and higher)

The WebMO apps supports all chemistry courses by calculating and displaying:

  • VSEPR structures for General Chemistry
  • 3-D structures to replace model kits for Organic Chemistry
  • Data and properties for Analytical Chemistry
  • Point group and symmetry elements for Inorganic Chemistry
  • Small proteins and bimolecules for Biochemistry
  • Molecular orbitals and vibrations for Physical Chemistry
  • WebMO calculations for undergraduate and graduate level Research

Thousands of students and scientists use the WebMO apps on their smartphones and tablets each month.  You can join them today for free!

WEBMO SUPPORTS CLOUD COMPUTING

More computational services are moving away from local hardware and into the "cloud".  Cloud computing requires zero upfront capital outlay, eliminates hardware maintenance, and can dramatically lower the cost of computing.

WebMO now supports installation on cloud computing platforms.  In less than 10 minutes, you can use your web browser to create a virtual machine, run the WebMO SITC ("Server in the Cloud") script, and have a functioning WebMO 16 server.

The cost of a WebMO cloud server can be amazingly low: <$1 per day for a WebMO server capable of running jobs on standard ab initio chemistry engines, and just $0.12 per day for a WebMO server running MOPAC!  And when you don't need it, you just turn it off.

Complete documentation is available at http://www.webmo.net/cloud/sitc.html

Since Google Compute Engines are free for the first 60 days, so there is no cost or risk to try cloud computing today.


Comments

BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

 

Sampling conformational space is a key requirement for several areas of ligand design in small molecule drug discovery. A recent paper BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library DOI describes a new conformational search method.

The project homepage provides a download, supports Mac OSX 10.4 or higher.

Comments

CCP4 released

 

The current version is CCP4 7.0 (07 January 2016). The new packages include:
SHELX suite: co distribution for academic users
CCP4I2: new ccp4 interface
DIALS: data processing and integration
ARCIMBOLDO-LITE: molecular replacement pipeline
The updated packages include PHASER, XIA2, REFMAC, MONOMER LIBRARY, AMPLE, COOT, AIMLESS POINTLESS, CTRUNCATE, DIMPLE, BLEND and many more

CCP4 exists to produce and support a world-leading, integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques.

The latest version supports Mac OSX and Linux and requires X11. Source code is also available.

Comments

An early Christmas present from Chemical Computing Group

 

Chemical Computing Group have just released an up date to MOE, version 2015.10 includes:-

Protein-Protein Docking

  • Generate docked poses using FFT followed by all atom minimization
  • Define receptor and ligand sites to focus docking
  • Automatically detect antibody CDR sites

Integrated Alignment, Consensus and Superposition in the Sequence Editor

  • Manipulate multimeric protein sequences using split side-by-side Sequence Editor panes
  • Use dendrograms to visualize pairwise similarity, identity and RMSD relationships
  • Select residues based on plotted values using resizable sequence editor plots

Distributed Pharmacophore Searching

  • Run pharmacophore searches on a cluster directly from MOE GUI
  • Perform fast corporate database searches
  • Access multiple databases stored on a central server

Covalent Docking and Electron Density Docking

  • Use reaction-based organic transformations to covalently docking
  • Minimize ligand strain energy while maximizing ligand fit to electron density
  • Run docking through an enhanced streamlined scenario-based interface

Extended Hückel Descriptors and pKa Model

  • Compute molecular properties such as logP, logS and molar refractivity
  • Determine populations of ligand protonation states at a given pH
  • Calculate the pKa and pKb of small molecules

13C NMR Analysis

  • Apply QM conformation refinement to calculate 13C NMR shielding
  • Convert computed shieldings and predict 13C NMR chemical shifts
  • Compare computed chemical shifts to experimental shifts for structure determination

I'll write a review in the New Year.


Comments

BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library

 

I just thought I'd flag a recent paper on sampling conformation space DOI.

The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships.

The software is available from the MeilerLab home page

Comments

OpenEye Toolkits v2015.October released

 

OpenEye have announced the release of OpenEye Toolkits v2015.October. These libraries include the usual support for C++, Python, C# and Java.

New Features

  • FastROCS TK was added to the OpenEye toolkits collection
  • Molecule reading performance improvement in OEChem TK
  • The capabilities of the OEBio-Fragment Network have been expanded
  • 213 new ring templates have been added to the OEChem TK built-in ring dictionary

The full release notes give more details

In particular note the 2015.Oct release is the last to support Mac OSX 10.8 so time to upgrade if you have not already done so.

Comments

Computational chemistry guides & tools

 

The Medicines for Malaria Venture have an interesting page in which they are accumulating a list of computational tools and guides describing the use of the tools to address key issues within the drug discovery process.

Tools were chosen to address common needs expressed by medicinal and computational chemists working in the not-for-profit area. Recognising that this is a global effort, we have selected software packages on the basis of being free for all users.

The guides are either text descriptions or webcasts showing the tool in action. To date they include DataWarrior, KNIME, YASARA, ChEMBL and PK Tool.

Comments

Dalton 2015 entry updated

 

The Dalton2015 suite consists of two separate executables, Dalton and LSDalton. The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilities.

Together, the two programs provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2015 suite.

Dalton can be run on a variety of systems running the UNIX operating system. The current release of the program supports Linux, Cray, SGI, and MacOS using GNU or Intel compilers (we plan to publish patches for PGI and XL compilers).. The program is written in FORTRAN 77, FORTRAN 90 and C, with machine dependencies isolated using C preprocessor directives. All floating-point computations are performed in 64-bit precision, but if 32-bit integers are available the code will take advantage of this to reduce storage requirements in some sections.

Comments

wxMacMolPlt updated

 

The popular GUI for GAMESS MacMolPlt has now been renamed and moved to GitHub, wxMacMolPlt is a cross-platform (Mac OS X, Linux and Windows) GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties

page5_blog_entry1790_1

wxMacMolPlt can be downloaded from here

Bode, B. M. and Gordon, M. S. J. Mol. Graphics Mod., 16, 1998, 133-138. DOI

Comments

SeeSAR version 3.2 released

 

SeeSAR 3.2 can now be used in cases where there is no protein. For example if for the analysis of a ligand-based virtual screen

ceeibecg

Release Notes version 3.2 2015-07-24

Utilizing SeeSAR without a protein

  • SeeSAR has grown from a single purpose affinity assessment tool to a multi purpose 3D structural viewer for compound design and prioritization. With this update it is now also possible to use all these nice features for 3D ligand-based projects. You may, for example, visually inspect small molecules alignments. You may filter a hit list by means of calculated and external properties...
  • Big data booster, With version 3.0 we first equipped SeeSAR with database functionality. Version 3.2 comes with a load of performance enhancements that speed up the calculation by up to a factor of 5, now utilizing all available CPUs in your computer even more efficiently.
  • 3D graphics enhancement, In this version we updated the graphics support and SeeSAR is now compatible with more graphics cards than ever before. Especially the compatibility with integrated graphics cards (the type most frequently found in laptop computers) - which used to be the major trouble makers - has been greatly improved.
Comments

Kinetiscope, interactive method for the accurate simulation of chemical reactions.

 

Kinetiscope is a scientific software tool that provides the bench scientist with an easy-to-use, rapid, interactive method for the accurate simulation of chemical reactions.

ferricyanide

The program package is completely self-contained, and requires no programming or extensive user training. This lets you become immediately productive,

Kinetiscope comes with a User's Manual, a set of tutorials and an extensive library of example simulations that show you the kinds of systems that can be studied with it and that illustrate techniques for handling various types of physical situations. The library includes simulations of gas phase, solution phase and solid state reactions such as co- and terpolymerization ... radical chain-initiated polymerization (including a sample spreadsheet for extracting molecular weight distributions) ... kinetic resolution of enantiomeric mixtures ... chemistry in supercritical media ... pH-dependent model enzyme kinetics ... thermogravimetric analysis ... temperature programmed desorption ... smog chemistry ... silane chemistry in a chemical vapor deposition reactor ... model batch and flow catalytic reactors ... curing of polymers with significant volume shrinkage ... synthetic protocols for preparation of a photosensitizer ... chemical oscillators ... electrochemical reactions studied by cyclic voltammetry ... photochemical reactions from a pulse light source ... pharmacokinetics of drug dosing ... and imaging chemistry in photoresist materials.

Kinetiscope is a 64-bit application and requires Mac OS X 10.6 or above.

  • D. L. Bunker, B. Garrett, T. Kliendienst and G.S. Long III, Combustion and Flame 23, 373 (1974).
  • D. T. Gillespie, Journal of Computational Physics 22, 403 (1976).
Comments

Workshop on Resources for Computational Drug Discovery

 

I just thought I'd mention this upcoming workshop, as ever there is a top class line up.

EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery 2-6 November 2015 Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=510

The draft agenda is here

Comments

SeeSAR Updated

 

SeeSAR has been updated to version 3.1, the release notes highlight two significant new features.

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution.

  • Working with "big data" With this update we lifted the limit of handling only a maximum of 5000 poses in SeeSAR. We know that a lot of people like to do their compound analysis and prioritization after virtual screening campaigns also with much bigger sets. It is not likely that you will look at more than a couple of hundred poses, however, since the filtering (see also below) is extremely efficient, it provides quite an attractive opportunity to load all your data (not just the top x) and do your prioritization with all properties at hand right here in SeeSAR.
  • Enhanced filtering Behind the scenes SeeSAR knows so much more about your compounds than what is displayed in the table. The basic stuff like no. of acceptors and donors, rotatable bonds, etc. to do the usual Lipinski-type filtering is of course available, but also more elaborate stuff like the number of hydrogen bonds formed or the number of torsions that lie outside the statistical "norm". All of these are now available for filtering to help you optimally trim down your data to find the really interesting part.

NOTE! SeeSAR project files from older versions are incompatible and cannot be loaded. By default SeeSAR puts a new version in a separate location. The recommendation is to export your data from the old project file with the old version and import it into the latest SeeSAR. This is a one-time effort, which allows you to benefit from the features of the most up-to-date version.

Comments

Findings and SZMAP updated

 

Findings 1.2.3 the electronic notebook has just been released. Already using Findings? Menu Findings Check for updates...

OpenEye have just announced the release of SZMAP v1.2.1. This is a critical upgrade that fixes several bugs.

  • The Water Orientation VIDA Extension now saves orientation probability data and ensemble energy, vdw and order data on probe molecules as SDData. When probes generated by this extension are written to an .sdf file, these values will be written as well.
  • The Water Orientation VIDA Extension (version 1.1.3) now displays the correct water orientations for results from szmap version 1.2.0. It is also more compatible with 2D depictions in the 3D display.
  • gameplan no longer crashes when all stabilization test sites clash.
  • pch option -nonsymmetrized_charges now works to control AM1BCC partial charges. The default has been changed to true so as not to alter the default behavior.
  • pch no longer treats CYS residues bonded through the sidechain to a non-CYS as anionic.
  • pch no longer duplicates non-standard groups containing a metal (such as cofactors) and groups they are bonded to.
  • The hydrogen charge on the standard water probe is now correctly listed as +0.327 not +0.237 in SZMAP Theory.
Comments

Cresset update Torch and Forge

 

The update of Forge, a computational chemistry workbench for ligand-based design, includes over 170 new or improved features. Of particular note is Activity Atlas a new component enables you to summarize the SAR for a series into a visual 3D model that can be used to aid new molecule design. Forge V10.4 can now connect to an external web service, through a REST interface, to import external properties and data computed or retrieved by such web services as additional columns in the Molecules Table.

The latest version of Torch now includes Multi-parameter Optimization (MPO) options including condensing many activity and physicochemical properties into a single score representing the fit to the project profile, this has been coupled to an improved radial plot visualisation and tile display.

Comments

OpenEye toolkits updated

 

OpenEye has announced the release of OpenEye Toolkits v2015.June. These libraries include the usual support for C++, Python, C# and Java and are now available for download.

New Features Highlights:

  • PDB Splitting in OEBio TK
  • PAINS (Pan Assay Interference Compounds) filter in OEMolProp TK
  • Matched molecular pair improvements in OEMedChem TK
  • Custom ring template dictionaries in OEChem TK
  • Anaconda support for easier Python toolkit installation
Comments

AMBER Tools

 

The recently updated AMBER tools now includes software to analyse the structure and thermodynamics of water at protein and other surfaces. In addition to 3D-RISM, AMBER Tools now includes a new method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites.

The method is described in this paper, Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril DOI.

Solvation and desolvation plays a critical role in ligand binding but can be difficult to determine computationally.

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.

Comments

Gamess-US on a Raspbery Pi

 

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. In an interesting development it is now possible to compile Gamess-US on the $40 Raspberry Pi, full instructions are available here. This provides a low cost system for demonstrating quantum chemistry.

To aid construction of the chemistry input WebMO-14.0, a web-based interface for computational chemistry programs, now has an App for iPhone/iPad. This allows you to compose e.g. a Gamess computation on your iPad or iPhone and send it to your Raspberry Pi (in the local network or on the web with a forwarded IP) to run the job and get the results back for visualizing and printing.

gammespi

Comments

MacMolPlt 7.6

 

I just got this message regarding MacMolPlt a graphics program for plotting 3-D molecular structures and normal modes (vibrations).

I have just finished posting the final binaries for MacMolPlt 7.6. In addition to the code changes I have had to move the home site and binaries download sites due to the impending shutdown of Google code.

This version includes the following changes:

  • Energy plot window now accepts the same keystrokes as the main display window to change frames (left, right, home, end)
  • Fix a parsing issue with ROHF GAMESS log files
  • Account for an $EFRAG group change to allow all fragment atoms rather than only the first three.
  • Fixed a crash in the frequency window (when no normal modes are present)
  • Fixed the positioning of lone pairs in the builder when the coordination number plus the number of lone pairs is 5.
  • Fixed a couple of parsing issues with MolDen and Molekel (mkl) files.
  • Added GIF and TIFF export image formats (requires wxWidgets 2.9 or newer).

I have also reworked the 3D orbital generation code to significantly improve performance. Please report anything that doesn't look quite right.

Binaries and source files are available at: http://brettbode.github.io/wxmacmolplt/

Comments

Lucas, Molecule viewer and editor

 

Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.

lucas

Journal of Cheminformatics 2015, 7:16 [DOI](http://dx.doi.org/10.1186/s13321-015-0060-z}

The source code is available on Sourceforge

Comments

Scientific Applications under Yosemite

 

I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.

Comments

MOE updated

 

MOE2014.0901 Update is now available. MOE is a fully integrated molecular modelling and drug discovery software package.

MOE 2014.0901 updates:

Enhancements:

Protein Builder

  • Option for AMBER residue name
  • Append/prepend multiple residue sequence specified by single-letter names Builder:
  • Added H’s inherit color if there is a consistent coloring in the residue

sddesc: New -smi:p option causes field headers to be written to the output ASCII file

Bug Fixes:

  • MOESVLRUNPATH now properly honored
  • Combinatorial Builder now honors different attachment point locations on the same R-group
  • Database Save As one entry per file mode now properly generates unique filenames
  • Dock Template Forcing batch file now correctly generated
  • Saved views in .moe files now properly restored
  • Auto-save when Database Viewer display attributes are changed can now be disabled to prevent changes to the database file modification date when only the display is changed and not the database content
  • SVL function Deprotonate now works properly
  • Various MOE Project and Project Database Update bugs
  • Various minor bug fixes

There are reviews of MOE available here

Moe:- Molecular modeling
Moe Update (Jan 2009):- Molecular modeling
Review of MOE (2009.10 release):- Molecular modeling
Moe Update (December 2010.10 release):- Molecular modeling
Moe Update (December 2011 release):- Molecular modeling
Moe Update (December 2012 release):- Molecular modeling

Comments

MOE updated

 

The molecular modelling platform MOE 2014.09 has been updated, some of the new features in MOE include:

  • MOE Project for Organizing SBDD Data
  • Focused Protein and Antibody Libraries - Virtual Phage Display
  • Quantum Mechanical Refinement of Conformations and Energy Minimization
  • Template Forced Docking and Molecular Superposition
  • Non-natural Amino Acid Support for Protein and Peptide Design
  • Specialized Protein Family Databases and Search Interface

MOE is a software system designed to support Cheminformatics, Molecular Modelling, Bioinformatics, Virtual Screening, Structure-based-design and can be used to build new applications based on SVL (Scientific Vector Language).

There are several reviews of the previous versions of MOE here

Comments

Ocura (aka StarVue)

 

Previously known as StarVue, the latest release of Ocura, version 6.0, is now available. This latest release will enable you to open and view files from the latest releases of StarDrop 6.0 and Sentira 1.0.

Ocura is a desktop application is specifically designed for scientists who want a simple way to load a set of molecule structures and easily browse through the data.

Comments

POSIT updated

 

OpenEye ihave announce the release of POSIT v3.1, the component of the OEDocking suite devoted to pose prediction.

This update includes:

  • The HYBRID and FRED algorithms have been incorporated into POSIT, the appropriate method is determined by analyzing the ligand to pose against the input receptors.
  • Multiprocessing has been enabled through the use of MPI, to speed calculations.
  • POSIT now supports a list of receptors files or .lst file as input. This overcomes command-line limitations for the number of receptors that can be used simultaneously.
  • Added a MEDIOCRE result rating for results between 33% and 50% probability.
  • Command line parameters have been simplified and updated to be compatible with the OEDocking Suite of tools.

POSIT is designed for the posing problem in lead optimization, i.e. how best to leverage project information from previous protein-ligand structures to predict the pose of a new ligand. It does this by assessing the similarity of the new ligand to known bound structures. Performance degrades as similarity decreases and so at some point it is worth searching more exhaustively.



Comments

SeeSAR updated

 

SeeSAR 1.5 has been released. SeeSAR it is intended as an interactive tool for designing/improving ligands for drug discovery.

The latest release covers two major topics: 1. A series of features that make the editing more swift and easier. To this end they introduced hot-keys, context menus and drawing a bond by drag&drop. 2. Often times people use SeeSAR for visual inspection e.g. after docking. Now normally you'll have multiple poses per compound. For a better overview the Table now allows you to collapse all poses to just one line per compound.

cihhbjhj

Furthermore you can set a bookmark to indicate what you like and export only the ones on the wish list.

There is a review of SeeSAR here.

Comments

FORECASTER, docking tool

 

I just got this email

Thank you for your collaboration in helping us to test the beta version of the FORECASTER Suite 2014. From your feedback and bug reports, we have now released the final version of the Suite. The files were updated and posted on the download page. Please send us any bugs that you might have not yet reported.

The FITTED docking tool was initially been developed as a suite of three programs: SMART (used to prepare the small molecules for docking), PROCESS (used to prepare the protein files for docking) and the docking program FITTED. More recently, these three programs together with several others have been integrated into a single package, namely FORECASTER.

More information can be found here http://fitted.ca/download.html#forecaster

Comments

2014 release of the ADF modeling suite

 

The ADF modeling suite consists of the GUI, the powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), the semi-empirical DFTB and MOPAC2012 modules, ReaxFF, and COSMO-RS. The binaries for the entire suite work out of the box, in parallel, on all popular platforms (Windows, Mac, Linux).

A summary of new features and improvements in the 2014 release:

  • lower-memory, better parallel SCF in ADF
  • significant speed-ups in DFTB and the periodic DFT code BAND (AO-based)
  • many-body dispersion functionals (Tkatchenko et al.)
  • conformer search, support for multiple configurations, spectra averaging
  • TD-DFTB and DFTB-NEGF, with electronic parameters for 87 elements
  • ReaxFF force field optimizer, Grand Canonical Monte Carlo
  • COSMO-SAC 2013-ADF parameters
Comments

KiSTheIP added to alphabetical listing

 

KiSThelP is a cross-platform free open-source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, NWChem). Some key features are:

  • gas-phase molecular thermodynamic properties (offering hindered rotor treatment)
  • thermal equilibrium constants
  • transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart)
  • RRKM rate constants, for elementary reactions with well-defined barriers.

KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the GUI and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D-plots, exporting images and data files.

Comments

Sentira Review

 

Sentira is a new chemical data visualisation tool from Optibrium. The focus is on ease of use data visualisation and as such is probably targeted at the bench scientist rather than a specialist computational scientist. It supports a selection of plotting and SAR tools.

I’ve written a review of my first impressions.

There is also a list of data visualisation applications here.

Comments

Chargemol

 

Chargemol program performs atomic population analysis to determine DDEC net atomic charges, atomic spin moments, and effective bond orders. Because the DDEC net atomic charges are simultaneously optimized to reproduce atomic chemical states and the electrostatic potential surrounding a material, they are well-suited for constructing force-fields used in atomistic simulations (e.g., classical molecular dynamics or monte carlo simulations) and for quantifying electron transfer between atoms in complex materials and during chemical reactions

The DDEC method is described in the following publication and references therein.

Thomas A. Manz and David S. Sholl, "Improved Atoms-in-Molecule Charge Partitioning Functional for Simultaneously Reproducing the Electrostatic Potential and Chemical States in Periodic and Non-Periodic Materials", J. Chem. Theory Comput., Vol. 8 (2012) 2844-2867. DOI

The program can be run using either Matlab or Fortran source codes, which yield identical numbers. The Fortran code is parallelized with OpenMP and runs much faster than the Matlab code.

Comments

Quantum Expresso Updated

 

Quantum Expresso 5.1 is available for download.

QUANTUM ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modelling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Comments

New additions and updates

 

McQSAR:  A Multiconformational Quantitative Structure−Activity Relationship Engine Driven by Genetic Algorithms

McQSAR, an extension to the traditional GA approach to derive QSARs. McQSAR is able to use descriptors for multiple representations per compound, such as different conformers, tautomers, or protonation forms. Test runs show that the algorithm converges to a set of representations that describe the binding mode of the set of input molecules to a reasonable resolution provided that suitable descriptors based on the three-dimensional structure are used.

Mikko J. Vainio and Mark S. Johnson (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J. Chem. Inf. Model. 45, 1953-1961 DOI.

The recently updated Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.

Comments

Installing ACPC on a Mac

 

One of the advantages of using a Mac for science is that you can often make use of the UNIX underpinnings of Mac OSX to access programs written for Linux.

A recent publication in Journal of Cheminformatics caught my eye, screening of molecules using electrostatics is usually a very time-consuming process, but this publication describes an interesting and very quick way to screen molecules.

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening Francois Berenger, Arnout Voet, Xiao Yin Lee and Kam YJ Zhang Journal of Cheminformatics 2014, 6:23 doi

I’ve written instructions for how to install ACPC under Mac OSX.

Comments

A Review of Forge V10.2 on the New MacPro

 

Now that I have my new MacPro I thought it might be interesting to try out a couple of the software packages that I’ve previously reviewed. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds. I’ve previously reviewed ForgeV10 and as it was formally known FieldAlign so I’m going to focus on the support for multiple processors and a few of the new features.

Read the review here

forge2

There is a compilation of software reviews here



Comments

Amber 14 and Amber 14 Tools released

 

Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
  • More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual
Comments

Porting of BUDE (Bristol University Docking Engine) to OpenCL.

 

A recently publication “High Performance in silico Virtual Drug Screening on Many-Core Processors” DOI describes porting BUDE (Bristol University Docking Engine) to OpenCL.

Our highly optimized OpenCL implementation of BUDE sustains 1.43 TFLOP/s on a single NVIDIA GTX 680 GPU, or 46% of peak performance. BUDE also exploits OpenCL to deliver effective performance portability across a broad spectrum of different computer architectures from different vendors, includ- ing GPUs from NVIDIA and AMD, Intel’s Xeon Phi and multi-core CPUs with SIMD instruction sets.

BUDE is now one the fastest HPC applications ever developed and nicely demonstrates the portability of OpenCL across different architectures.

There is a list of GPU accelerated applications here.

Comments

Academic access to CrunchYard HPC

 

CrunchYard is pleased to announce their academic offering for HPC in the cloud. The academic offering allows anyone with a valid academic e-mail to instantly access the online HPC facility.

Group accounts can be created for your research group, where simulation credits are shared. Credits are valid for 2 months after purchase.

Academic accounts include access to over 300 true CPU cores, and the following simulation software: FEKO CP2K NWCHEM GAMESS GROMACS LAMMPS

Other licensed codes are available on request (such as CPMD, STAR-CCM+ etc.)

Comments

Asteris and RCSB PDB updated

 

The official mobile app for viewing PDB structures RCSB PDB has been updated to include the April molecule of the month.

The molecule designer app Asteris has been updated to version 1.0.1 with a number of bug fixes and performance improvements.

screen480x480

Comments

GTKDynamo:- Molecular modeling extension for PyMOL

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

  • Pure QC simulations - ab initio and SMO.
  • Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
  • Hybrid QCMM simulations.
  • Single point calculations.
  • Energy minimization.
  • Molecular dynamics.
  • Reaction coordinate scanning.
  • Umbrella sampling.
  • Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

  • pDynamo
  • Matplotlib
  • Numpy / Pylab
  • Pymol 1.x
  • pyGTK
  • ORCA, ab initio calculations.

GTKDynamo_overview-page001_800

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

Comments

QMForge 2.3.2 released

 

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03/09, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported. The following analyses are available:

  • The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, Molpro, and ORCA,
  • Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
  • Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital,
  • Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
  • Frenking’s Charge Decomposition Analysis,
  • Calculation of Mayer's bond orders,
  • Visualization of each step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
  • Plots of Convergence and Energy in the Geometry Optimization tab,
  • A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
  • Animation of the normal modes of a frequency calculation and the ability to save these as animated GIFs,
  • Plots of IR and/or Raman spectra in the Frequency Tab, and
  • A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.

QMForge has been created using the following dependencies:

  • The Python scripting language (2.7.5),
  • The Qt4 toolkit and its Python extensions PyQt4,
  • NumPy (1.7.1),
  • PyQwt (5.2.0), and
  • The cclib computational library (v1.2b).
  • OpenBabel and its Python bindings
  • The Python Imaging Library (PIL)
  • simplejson

fragment_assignment

QMForge has only been extensively tested on Mac OS X Snow Leopard and Mavericks

Tenderholt, Adam L. QMForge, Version 2.3.2, http://qmforge.sourceforge.net.
Tenderholt, Adam L. "QMForge: A Program to Analyze Quantum Chemistry Calculations", Version 2.3.2, http://qmforge.sourceforge.net.

Comments

Schrodinger Small Molecule Drug Discovery Suite Updated

 

The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
phase
fqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical.py script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see http://tech.knime.org/whats-new-in-knime-29 for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.

Comments

MolSoft Releases ICM Version 3.8

 

MolSoft have announced that a new version of ICM is now available for download from the support site . A description of the key new features can be found on the news page and release notes. To help you get to know the new features we will be holding a free webinar next week (2/11) - we hope you can join us, please register here.

Some of the key new features include:

  • Anaglyph Stereo
  • MolSkin - high quality surface graphics
  • Movies from Slides
  • SCARE - induced fit docking
  • Fragment screening
  • MolScreen - >360 high quality fingerprint and 3D pharmacophore models
  • Blast search direct from the GUI
  • ToxScore - new score for drug reactivity and toxicity
Comments

QMForge 2.3.1 released

 

QMForge 2.3.1, a cross-platform, open-source program for interpreting and analyzing the results of QM calculations has just been released

QMForge 2.3.1 builds upon the previous versions with the addition of the following features:

  • Plots of Convergence and Energy in the Geometry Optimization tab,
  • Plots of IR and/or Raman spectra in the Frequency Tab,
  • Ability to save the normal modes of a Frequency calculation as animated GIFs,
  • Gross Population Analysis to compare Mulliken and Lowdin populations and spin densities for each atom and orbital

Other notable features include

  • The support of several QM output formats including Gaussian, ADF, GAMESS (and its various derivatives), Jaguar, and ORCA,
  • Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on user-defined sets ("fragments") of basis functions,
  • Fragment Analysis to interpret the contributions of fragment MOs to molecular MOs,
  • Charge Decomposition Analysis,
  • Mayer's bond orders,
  • Visualization of every step in a geometry optimization, with the ability to save any of those structures as XYZ or PDB files,
  • A simple, yet powerful, XYZ editor with tools that allow translations and rotations to align bonds to specific axes,
  • Animation of the normal modes of a frequency calculation, and
  • A plot of electronic transitions and a easy-to-read list of the corresponding orbital excitations from TDDFT/CIS calculations.
Comments

A review of FAst MEtabolizer (FAME)

 

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues to resolve in drug discovery often revolve around absorption, distribution, metabolism and excretion (ADME). Whilst we can measure the levels of parent drug in various medium tracking metabolic fate can often be a considerably more difficult proposition requiring significant resources. For this reason prediction of sites of metabolism has become the subject of current interest.

FAME DOI is a collection of random forest models trained on a comprehensive and highly diverse data set of 20,000 small molecules annotated with their experimentally determined sites of metabolism taken from multiple species (rat, dog and human). In addition dedicated models are available to predict sites of metabolism of phase I and II processes.

aspirinFame

FAME offers a high performance prediction of sites of metabolism mediated by a wide variety of mechanisms.

The full review is available here

There is a list of software reviews here.

Comments

MOE Update

 

Chemical Computing Group have just announced an update for MOE.

A patch update is now available for MOE 2013.08. This patch contains a series of important updates for better performance, s

In the MOE 2013.0801 patch update:

  • System Manager browsing speed-up for large systems
  • System Manager tag/group expansion only on Ctrl-click during browsing
  • Mac OS X NVIDIA graphics driver bug workaround
  • Mac OS X real-time ray tracing now supported by default on the new Intel Iris and Intel Iris Pro graphics cards
  • Bug fixes
Comments

Computational Chemistry Freeware

 

I recently came across this brilliant collection of software from Michel Petitjean

  • ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
  • ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
  • CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
  • CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
  • CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
  • DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
  • DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
  • GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
  • MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
  • POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
  • POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
  • QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
  • RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
  • VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.

Binaries are available for MacOSX and Linux.

Comments

Crunchyard

 

I noticed that CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on Crunchyard expanding the list of available Computational Chemistry packages. The following packages are also available. CP2K, LAMMPS, GAMESS, GROMACS , NWCHEM

Comments

CPMD added to alphabetical listing

I’ve added CPMD to the alphabetical listing of applications.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.

Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

CPMD capabilities

  • Works with norm conserving or ultrasoft pseudopotentials
  • LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
  • Isolated systems and system with periodic boundary conditions; k-points
  • Molecular and crystal symmetry
  • Wavefunction optimization: direct minimization and diagonalization
  • Geometry optimization: local optimization and simulated annealing
  • Molecular dynamics: constant energy, constant temperature and constant pressure
  • Path integral MD
  • Response functions
  • Excited states
  • Many electronic properties
  • Time-dependent DFT (excitations, molecular dynamics in excited states)
  • Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.

Comments

SYBYL-X 2.1.1 released

 

SYBYL-X 2.1.1 is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.

  1. Hologram QSAR (HQSAR) is a now available via Python.  HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors.

  2. Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.

Comments

SZYBKI has been updated

 

OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

  • New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
  • A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
  • Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
  • Constraining torsion potential in the form: f8ebfd663514a377a56dfefaeb661230a663dc0f, where 81251f7be3a3c36e3c6602884accebe2d6ab3292 is the user specified force constant and 6b57c4a2f949d360120e9eec70ed44786c71b408 is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
  • New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
  • Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
  • New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
  • Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
  • Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.
Comments

MOE 2013.08 Released

 

Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).

General Updates

Extended Hückel Theory for Pharmacophore Discovery

  • Apply EHT strengths to identify and discover weak and strong interactions
  • Annotate non-standard interactions: halogen and CH bond donors
  • Score pharmacophore hits using sum of interaction energies

de novo Loop and Linker Modeler

  • Search and browse for de novo and knowledge-based loop candidates
  • Generate multiple loop conformations and score loop-loop interactions • Investigate linkers for fusion proteins and dual variable domains

Protein Alignments and Superpositions

  • Superpose protein structures independent of sequence
  • Apply new threading methodology for sequence to structure alignments
  • Align sequences and superpose structures using STOVCA criteria

Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.

  • Create additional data grouping level in System Manager
  • Handle large number of protein:ligand complexes in real-time
  • Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored

Interface to Mogul from CCDC

  • Access a knowledge-based library of small molecule crystallographic data
  • Visualize histograms and statistics fo rbond angles, dihedrals and torsions • Ensure ligand conformation is consistent with the CSD

Solvent Analysis using 3D-RISM Enhancements

  • Calculate water densities on full protein or protein:protein interface
  • Accurate placement and stability prediction of water sites
  • Use3 D-RISM densities to validate water position in crystal structures

chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies

Mac OS X Enhancements.

  1. OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations – Hide, Show, and Quit – across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.

  2. New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.

  3. Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.

Comments

Scripting Vortex 16

 

OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.

There are also a number of already built models that the public can access, these include

  • Ames test
  • CYP1A2 inhibition
  • LogP and Solubility

You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.

Comments

Turning up the heat with Torch and Forge

 

Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-

“What is the largest change that can be made whilst maintaining activity?”

Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge. Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

Activity Miner1

More details are here

Comments

ROCS Updated

 

OpenEye have just announced that the virtual screening tool ROCS v3.2 has been released.

Several noteworthy features have been added to this version including a -subrocs option that can drastically improve substructure alignments. Also included is an application rocs-report that uses our 2D depiction technology to make pdf reports of hitlists displayed with 2D similarity, shape and color overlaps, as well as property histograms. Substantial upgrades have been made to vROCS. An improved sketcher now highlights unspecified stereochemistry in atoms and bonds in query structures, and requires the user to correct any unspecified stereochemistry.

ROCS is available for download here.

Comments

StarDrop 5.4

StarDrop was recently updated to version 5.4, this brings an update to the virtual library design module and scaffold based design, there have also been improvements to the plotting and data visualisation.

There are now seven optional plugins with three exciting new options.

Derek Nexus™ - Knowledge based toxicity prediction The new Derek Nexus module for StarDrop provides Lhasa Limited's world-leading technology for knowledge-based prediction of key toxicities. Using data from published and donated (unpublished) sources, Derek Nexus identifies structure-toxicity relationships that alert you to the potential for your compounds to cause toxicity. The Derek Nexus module provides predictions of the likelihood of a compound causing toxicity in over 40 endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.

BIOSTER™ - A world of chemistry experience BIOSTER is developed and updated in collaboration with Digital Chemistry and is available as an optional extension to StarDrop's Nova module. This combination enables you to quickly and easily search the comprehensive BIOSTER database to identify transformations that are relevant to your compounds. These can be automatically applied to generate novel structures with a high likelihood of biological activity and synthetic accessibility, prioritised against the property profile you require for your project. BIOSTER brings the collective experience of the chemistry community to help you to discover new active analogues of your compounds based on the tried and tested principle of isosterism. The BIOSTER module contains a unique compilation of over 20,000 precedented bioisosteric transformations, manually curated from the literature by Dr István Ujváry, complete with references to the original publications in which they are described.

torch3D™ The renamed torch3D module, using Cresset’s unique Field technology to understand and apply 3D Structure Activity Relationship (SAR), has been updated to include the latest version of Cresset’s XED force field providing insight into compounds’ 3D structures, biological activities and interactions.

These certainly significantly expand the potential utility of StarDrop, but note that these are not part of the standard install and may require additional licensing.



Comments

ORCA updated

ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.

New Features of Version 3.0: 

  • Improved efficiency in integral evaluation and digestion, thanks to Ed Valeev for the improved libint 2.0 library!
  • Improved parallelization, in particular for RI-DFT calculations.
  • The DLPNO-CCSD(T) near linear scaling local correlation method. It has led to the first CCSD(T) level calculation on an entire protein.
  • Explicitly correlated (F12) MP2 and coupled cluster methods using several approximations to boost the efficiency (They also work together with DKH/ZORA, COSMO etc.). Again many thanks for Ed Valeev for his countless contributions to this project.
  • Efficient analytic frequencies for RI-DFT, hybrid DFT, Hartree-Fock and MP2 (also featuring QM/MM Hessians, ECPs, DKH/ZORA, van der Waals corrections etc., COSX and RI approximations).
  • Interface to the large-scale DMRG program "BLOCK" developed by Garnet Chan and co-workers. it can be used together with the CASSCF module of ORCA.
  • The "HF-3c" method by Grimme and co-workers is a slightly parametrized Hartree-Fock variant that can be applied to very large systems and can achieve stunning accuracy.
  • Nonlocal van der Waals corrections have been implemented by the Grimme group
  • A range of modern functionals, including M06-2X, have been implemented by the Grimme group making use of the XCFun DFT library by Ulf Ekstrom.
  • Range corrected hybrid functionals have been implemented by the Grimme group
  • Coupled cluster densities and new coupled cluster methods like orbital optimized and Brueckner coupled cluster methods.
  • EOM-CCSD excitation energies for closed-shell systems.
  • MP2 electric and magnetic response properties (but no NMR yet).
  • A fully self consistent CASSCF method with spin-orbit coupling has been developed
  • The ROCIS module features a new approach to the calculation of complicated X-ray absorption spectra that are dominated by spin-orbit and multiplet effects
  • Natural transition orbital analysis for TD-DFT excited states.
  • Effective Hamiltonian (infinite order) extraction of EPR parameters from QDPT calculations using MRCI and CASSCF/NEVPT2.
  • The RIJCOSX-SCS-MP3 method.
  • Removal of near linear dependencies in the orbital basis set.
  • Improved overlap fitted COSX approximation.
  • Geometric counterpoise correction.
  • Finite nucleus for relativistic single point calculations.
  • Finite temperature SCF calculations and correct gradients.
  • Improved picture change theory for DKH magnetic property calculations.
  • Extended correlation energy extrapolation schemes making use of of LPNO methods.
  • Interface to NBO 6.0 and AIM.



Comments

Scripting Vortex and MOE

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.

The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.

The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.

Full details are here




Comments

Computational Chemistry Comparison and Benchmark Database

The Computational Chemistry Comparison and Benchmark Database (CCCBDB) has released version 16 at cccbdb.nist.gov. The CCCBDB is a collection of experimental and computed (by quantum methods)  ideal-gas thermochemistry for 1591 small molecules and atoms. The properties include enthalpy of formation, vibrational frequencies, geometries, rotational constants and dipole moments.



Comments

Firefly 8.0.0 released

Firefly (previously known as the PC GAMESS) is a freely available ab initio and DFT computational chemistry program developed to offer high performance on Intel-compatible x86, AMD64, and EM64T processors. Firefly package is being developed by the Firefly Project Team.

The Mac OSX version can be downloaded here together with installation notes and user and quick start guides.

Details of this major update can be found on the news page



Comments

Crunchyard

Can't afford your own super computer ? I’ve just been sent details of CrunchYard this service allows scientists and engineers to submit simulations and run them on CrunchYard's system through an easy to use web interface. By making use of CrunchYard's cluster it means you don't have to buy and manage your own equipment. A brief look suggests there are a range of Computational Chemistry applications.

CP2K
LAMMPS
GAMESS
GROMACS

When you register you get 20 credits free which should be enough to test things out, further credits can then be purchased. For most applications one credit seems to get you 1 CPU for an hour. The FAQ section also provides access to demonstration input files for each of the packages.

computer cluster



Comments

QUACPAC v1.6 released

OpenEye have announced the release of QUACPAC v1.6. This release incorporates several improvements and some bug fixes.

The chemistry of molecular interactions is a matter of shape and electrostatics, but doing electrostatics poorly is worse than doing none at all; accurate charges are required. Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage

Updated

  • molcharge now uses the -method parameter for selecting a charge model. All individual flags for charge models have been removed.
  • tautomers will now allow interconversion of [NH2+]= and [NH3+]-.
  • tautomers now has a -warts option. Enabling this options will number the output molecules with an @ symbol.
  • The default AM1BCC charge model in molcharge now lightly restrains the AM1 geometry optimization to the starting coordinates. This allows the important relaxation of bond and angle degrees of freedom while greatly reducing the potential to alter the molecule’s conformation away from its starting coordinates.
  • The AM1BCC charge models -method am1bccsym and -method am1bccspt in molcharge now symmetrize the partial charges over bond-topologically equivalent atoms, e.g. methyl hydrogens, in keeping with the original model. This is especially important with conformationally flexible molecules.
  • molcharge now has a .fail file to output molecules that do not charge correctly.
  • fixpka has been refined to reflect feedback from collaborators. In particular isoxazoles and oxadiazoles were added while pyrazoles and aryl sulfonamides were refined. Aryl sulfonamide refinement also incorporated changes based on newly obtained experimental data.



Comments

Overview of SCM tools

It is sometimes difficult to keep the website up to date with some of the software that I don’t use and so I was delighted when Fedor Goumans contacted me to highlight some of the updates at Scientific Computing and Modelling. While ADF is still SCM's most widely used program, SCM offers a comprehensive modelling suite consisting of several different tools.

IRspectrumFerrocene

I have written a brief overview here.

Here is a list of the reviews available.



Comments

Installing Decoy Finder under Mac OS X

DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.

decoyfinder

Having spent the weekend getting it to run under Mac OS X I thought I’d write it all up so others can hopefully do it a little more smoothly.

Installing Decoy Finder under Mac OS X



Comments

SZMAP Updated

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding.

  • Multiprocessor Support : Calculations can be performed much faster with szmap and gameplan by using multiple processor on a single machine and on different machines with the same operating system installed. Because of this and other improvements to the software, numerical results will differ slightly from those produced by previous versions and the set of points that are determined to be clashing may vary slightly. szmap is highly parallelizable—big calculations scale very well when run on large numbers of processors.
  • szmapgrid will now split out all szmap grids into separate files in one step when the options -outputall_format and -prefix are used.
  • szmap_report now supports a -resolution option to control the quality of the property maps.
  • gameplan now indicates the stabilization magnitude in the log.
  • To streamline the szmap program, the following obscure command line options have been eliminated: -onlyprotein, skipmodified, -proteincharge, -proteinhydrogen, -ligandcharge, -ligandhydrogen, -chargedmol, -noprobedata, -requireexplicit, -addneutral, -addvacuum, -details. There are more direct ways to perform each of the functions that they controlled. The simple help for options in each of the SZMAP applications and utilities has been streamlined.
  • The WaterColor VIDA Extension has been updated so that it no longer changes the scale of gameplan results in VIDA.
  • The Quick Start chapter is now called the Tutorial and has been reorganized to improve clarity.

Full details are here



Comments

SYBYL-X 2.1 released

The latest update to SYBYL-X has been released, version 2.1 is only supported on 64-bit systems. In addition Python 2.4 is no longer supported, if you are using the latest Mac OS X then you should have Python 2.5.1. To check simply type python in a Terminal window.

chrismacbookpro:~ chris$ python
Python 2.5.1 (r251:54863, Nov 13 2007, 11:10:08) 
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

The major changes in SYBYL_X are a New Job Control System which replaces Netbatch, giving a consistent interface that is implemented across all of SYBYL-X modules. This is compatible with popular job queuing systems like Oracle Grid Engine, LSF, and Torque, and provides improved multi-processor support for key applications (Surflex-Sim, Surflex-Dock, Topomer Search, and UNITY).

There have also been updates to the Molecular Data Explorer (MDE) including:

  • Set 3D Viewer preferences for the display of proteins
  • Switch the structure viewing between the 3D Viewer and SYBYL’s main graphics window
  • Mark compounds in the 3D Viewer
  • Mark compounds in the Grid Viewer
  • Use a right-click menu in the Grid Viewer
  • Display a regression line and or unity line in a Scatter Plot
  • Tile Viewers in a grid
  • Set precision of column data
  • Save structures to a database
  • Export structures and associated column data to a MOL2 file
  • Copy a table

The Python QSAR functionality is now accessible outside of SYBYL as standalone Python scripts. Results of the Python jobs can be read into SYBYL using the new readXML expression generator. See $TA_LIB/python/lib/python2.7/site- packages/tripos/qsarutl/README for more information.

QSAR Project Manager enhancements include the ability to:

  • Modify names of structure sets and descriptor sets via a right-click menu
  • Rename and delete items in the Project Data list via a right-click menu



Comments

MOPAC speed improvements

The research group headed by Prof. Dr. Gerd B. Rocha at the Federal University of Paraiba, Brazil, has been successful in implementing a significant speedup. Two modifications have been made: many of the old, slower, operations have been replaced by the Intel Math Kernel Library, and sections of the code have been parallelized to take advantage of multi-threading. Details of the modifications can be found here

Times, in seconds, for a single-point calculation run on a 2 x 2.93 GHz 6-Core Intel Xeon with 16Gb of 1333 DDR3 memory chips Mac Pro computer, using 12 of the 24 threads

Species #atoms Current MOPAC2012 MOPAC 2012 with MKL MOPAC 2012 with MKL and multi-threading
Naphthalene 18 0.02 0.15 0.02
(H2O)573 1719 3,082.23 584.78 79.3
1G6X 1455 8,612.57 1,240.48 142.07
1RNB (Barnase) 2066 34,372.13 4,108.87 411.26


The improved MOPAC is available and can be downloaded from  http://openmopac.net/

In MOPAC, proteins can be modeled using the MOZYME technique, however, that technique is limited to closed shell RHF calculations. This means that proteins with free radical sites, excited state proteins, and proteins containing iron, chromium or other transition metal atoms should not be modeled using MOZYME. The new MOPAC reduces the computation time so that conventional MOPAC methods can now be used for many proteins. This means that it is now practical to use conventional MOPAC methods - RHF-CI and UHF - for modeling most of the smallerproteins, and by implication that it will be possible to model many systems that currently cannot or should not be modeled using MOZYME.


Comments

eFindSite now available for MacOS X

eFindSite is a ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins and is described in detail in a recent publication. Brylinski M, Feinstein WP.  2013.  eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands. J Comput Aided Mol Des. 27(6):551-567 DOI It employs a collection of effective algorithms, including highly sensitive meta-threading approaches, improved clustering techniques, advanced machine learning methods and reliable confidence estimation systems.

fig

eFindSite is available as a webserver and a standalone software distribution, and as of yesterday it is now available for Mac OS X!

UPDATE

A reader sent in detailed instructions for installation

  • OS X has perl already installed (with XCode/Command Line Tools I think)
  • Install perl cpanm module:

    sudo cpan App::cpanminus

  • type yes for automatic configuration

  • Install other perl modules:

    sudo cpan File::Temp sudo cpan File::Slurp

  • zlib should already be installed

  • Download gzstream: http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz
  • Build gzstream:

    cd ~/Downloads/gzstream/ make

  • I couldn't manage to download f2c from the link provided - ftp.netlib.org seems to be down? (Should be www.netlib.org/f2c )

  • Found a mirror: http://netlib.sandia.gov/cgi-bin/netlib/netlibfiles.tar?filename=netlib/f2c
  • Download, untar, then also unzip libf2c.zip inside the f2c directory.

    cd ~/Downloads/f2c/libf2c/ make f2c.h -f makefile.u make -f makefile.u

  • Download libsvm: http://www.csie.ntu.edu.tw/~cjlin/cgi-bin/libsvm.cgi?+http://www.csie.ntu.edu.tw/~cjlin/libsvm+tar.gz

  • Build libsvm:

    cd ~/Downloads/libsvm-3.17/ make ar cr libsvm.a svm.o

  • Download eFindSite: http://brylinski.cct.lsu.edu/content/efindsite-standalone-package

  • Untar it. We then need to copy the dependencies into the lib directory:

    cp ~/Downloads/gzstream/gzstream.h ~/Downloads/efindsite-1.1/lib/gzstream.h cp ~/Downloads/gzstream/libgzstream.a ~/Downloads/efindsite-1.1/lib/libgzstream.a cp ~/Downloads/f2c/libf2c/f2c.h ~/Downloads/efindsite-1.1/lib/f2c.h cp ~/Downloads/f2c/libf2c/libf2c.a ~/Downloads/efindsite-1.1/lib/libf2c.a cp ~/Downloads/libsvm-3.17/svm.h ~/Downloads/efindsite-1.1/lib/svm.h cp ~/Downloads/libsvm-3.17/libsvm.a ~/Downloads/efindsite-1.1/lib/libsvm.a

  • gcc 4.4 is required to properly compile eFindSite (Xcode has 4.2.1 I think)

  • install MacPorts: http://www.macports.org/

  • update software repos:

    sudo port selfupdate sudo port install gcc44

  • in eFindSite Makefile (~/Downloads/efindsite-1.1/src/Makefile) change "CXX = g++" to "CXX = g++-mp-4.4"

  • Then build it:

    cd ~/Downloads/efindsite-1.1/src/ make



Comments

MacMolPlt 7.5 has been released

MacMolPlt 7.5 has been released

This version includes the following changes: 

  • Added support for H and I basis functions.
  • Fixed a crash under windows related to prototype selection with a single atom.
  • Fixed issue on OSX preventing quit from the dock icon from working.
  • Fixed a couple of cases where a 2D surface was not updated appropriately.
  • New splash screen - guess the orbital!

Binaries and source files are available here



Comments

QMForge 2.2 released

QMForge is a program used to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), PC-GAMESS, Jaguar, and ORCA files are supported (see below). The following analyses are available:

  • Mulliken Population Analysis (MPA)
  • C-squared Population Analysis (SCPA)
  • Löwdin Population Alanlysis (LPA)
  • Overlap Population Analysis (OPA)
  • Mayer's Bond Orders
  • Charge Decomposition Analysis (CDA)
  • Fragment Analysis

MPA, CSPA, LPA, and OPA require a user-defined set of fragments, and prints the percent contributions those fragments make towards each molecular orbital in the molecule. Mayer's bond orders calculates the bond orders between each pair of atoms in the molecule. CDA and Fragment Analysis require three or more calculations (one for the entire molecule, and two fragment calculations), and provide information about the bonding interactions between fragments.

optimization-mac



Comments

Molegro Virtual Docker Update

An update to the Molegro Virtual Docker has been announced. It includes new data analysis tools that are now available directly from within Molegro Virtual Docker. Some of the new features include:

  • New and powerful regression features: Support Vector Machine regression and Partial Least Squares
  • Classification using either K-Nearest Neighbors or Support Vector Machine classification
  • Automated fine-tuning of regression and classification model parameters
  • Spring-Mass Maps for visualization of high-dimensional data
  • Clustering of data sets and subset selection
  • Principal Component Analysis
  • Outlier Detection



Comments

OpenEye updates

OpenEye have announced updates to a couple of their products

OMEGA v2.5 is designed to produce high quality multi conformer databases.

Highlights from this release include: OpenMPI version 1.6 is supported on all platforms. The -mpinp and -mpihostfile flags are now used to run OMEGA and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled. Now using -fixsmarts without -fixmol will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol will continue to match against the fixmol and use that match for the entire calculation.

EON v2.2. compares electrostatic potential maps of pre-aligned molecules and determines the Tanimoto measures for the comparison.

Highlights from this release include: OpenMPI version 1.6 is supported on all plafforms. The -mpinp and -mpihostfile flags are now used to run EON and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter. Now SD tags are prefixed with EON_. The tags are optional with the -sdTags parameter. Additionally, any existing ROCS tags will not be removed because ROCS and EON tags no longer conflict



Comments

Running LigPlot+ under Mac OS X

I occasionally get asked to help with non-Mac applications and recently someone inquired about LigPlot+.

LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs.

  • LIGPLOT - automatically generates schematic diagrams of protein-ligand interactions for a given ligand in a PDB file.
  • DIMPLOT - plots interactions across a selected protein-protein or domain-domain interface.

Whilst this application is supported under Windows and Linux there is no official support for Mac OS X, however since the GUI LigPlot is written in java and LIGPLOT is written in C there seems to be no reason why it should not run under Mac OS X and with a couple of tweaks it seems to run fine. Full details are here

interactionplot

Added to the list of Hints and Tips



Comments

Schrödinger Software Release 2013-1

Schrödinger have just announced the latest release of their entire suite of software programs, this covers tools for drug design, material science, biological modelling and general purpose modelling.

There are a huge number of new features and improvements in the small molecule drug discovery suite as well as Materials Science. However a couple of features caught my eye, pKa prediction for both rule-based and QM-based methods has been improved. Covalent ligand docking has been added and includes a variety of common docking chemistries. Improved pi-stacking interactions in docking. The molecular dynamics has been updated and now includes support for GPU-acceleration. The QM tools look to have been updated and the interface improved. ADME tools have been updated and in particular P450 site of metabolism has improved accuracy.

Predictive capabilities that can be applied across a wide range of chemical systems, including ,Reaction thermochemistry and reaction path exploration ,Rate constants for reactions and transport from transition state theory ,Validated models for calculating oxidation and reduction potentials, Accurate heats of formation and atomization energies for larger systems, Reliable properties for systems containing transition metals,Efficient calculation of electric field dependent properties,Prediction of vibrational and electronic spectra for complex systems,Multiple pre-defined calculation modes representing tested simulation parameters balancing speed and accuracy.

There has also been an update to PYMOL with improved rendering speeds and a couple of bug fixes.

This is certainly a great update and well worth having a detailed look at.



Comments

NWChem 6.3 released

An update to NWChem has been released with a host of new features.

NWChem 6.3 includes a new real-time, time-dependent density functional theory capability developed by Ken Lopata, EMSLs first William Wiley Distinguished Postdoctoral Fellow. This capability allows researchers to probe the ultrafast dynamical behavior of molecules and materials in response to an applied electric field.

With this release, researchers will for the first time be able to perform large scale coupled cluster with perturbative triples calculations utilizing the NVIDIA GPU technology. A highly scalable multi-reference coupled cluster capability will also be available in NWChem 6.3.

EMSL Computing greatly expanded NWChem 6.3 plane wave capability with access to a large set of density functional and pseudopotentials or effective potentials, and a more extensive suite of functionality for the projector augmented wave methodology.

Latest set of basis sets in the Basis Set Exchange have been added to the NWChem basis set library.In addition, NWChem 6.3 includes a new set of reaction path methodologies, tools for various spectroscopies including Python scripts to post-process UV/Vis and core spectra. Binaries are not yet available but the source code and instructions for compilation on a Mac are available are available. You will need Xcode and gfortran 4.6.2 from http://gcc.gnu.org/wiki/GFortranBinaries#MacOS



Comments

PSI updated

PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms. PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.Several parts of the code feature shared-memory parallelization to run efficiently on multi-core machines. An advanced parser written in Python allows the user input to have a very simple style for routine computations, but it can also automate very complex tasks with ease.

Now at Beta4 this is the first public release.

The majority of PSI4 was developed on Mac and Linux machines. In principle, it should work on any Unix system; however, we have not tested extensively on systems other than Mac and Linux. There is not a Windows version of PSI4

Psi4: An open-source ab initio electronic structure program, J. M. Turney, A. C. Simmonett, R. M. Parrish, E. G. Hohenstein, F. Evangelista, J. T. Fermann, B. J. Mintz, L. A. Burns, J. J. Wilke, M. L. Abrams, N. J. Russ, M. L. Leininger, C. L. Janssen, E. T. Seidl, W. D. Allen, H. F. Schaefer, R. A. King, E. F. Valeev, C. D. Sherrill, and T. D. Crawford, WIREs Comput. Mol. Sci. 2, 556 (2012). (doi: 10.1002/wcms.93).



Comments

FastROCS updated

I just got an email from OpenEye announcing an update to FastROCS.

FastROCS is an extremely fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. It uses a smooth Gaussian function to represent the molecular volume [1], so it is possible to routinely minimize to the best global match.

Features

  • Processes 2 million conformations per second on a Quad Fermi box
  • Returns overlays based on the quality of the 3D shape match against the query
  • Overlays are intuitive and visually informative when viewed in standard visualizers (e.g. VIDA)
  • Available as an XML-RPC based web service
  • Jobs can be launched and the subsequent results viewed directly from within VIDA
  • Reports rigorous Tanimoto measure between shapes

fastrocs



Comments

A Pan Assay Interference Compounds (PAINS) Filter for filter-it

A Pan Assay Interference Compounds (PAINS) Filter for filter-it

Jonathan B. Baell and Georgina A. Holloway published a very interesting paper on their analysis of frequent hitters from screening assays. DOI

This report describes a number of substructural features which can help to identify compounds that appear as frequent hitters (promiscuous compounds) in many biochemical high throughput screens. The compounds identified by such substructural features are not recognised by filters commonly used to identify reactive compounds. Even though these substructural features were identified using only one assay detection technology, such compounds have been reported to be active from many different assays. In fact, these compounds are increasingly prevalent in the literature as potential starting points for further exploration, whereas they may not be

In the supplementary information they provided the corresponding filters in Sybyl Line Notation (SLN) format, unfortunately I don’t use SYBYL and so needed them in SMARTS format for use with filter-it.

This article describes the process of creating a .sieve file for use with filter-it.



Comments

AmberTools13 (released on April 22, 2013)

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations (using NAB or mdgx), with either explicit water or generalized Born solvent models. It includes

NAB to build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models. Antechamber and MCPB Create force fields for general organic molecules and metal centers, tleap a basic preparation program for Amber simulations. sqm semiempirical and DFTB quantum chemistry program. pbsa Performs numerical solutions to Poisson-Boltzmann models. 3D-RISM Solves integral equation models for solvation. mdgx Code for explicit solvent molecular dynamics simulations. ptraj and cpptraj Structure and dynamics analysis of trajectories. MMPBSA.py and amberlite Energy-based analyses of MD trajectories.

AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers. The distribution contains a Reference Manual in pdf format.

New features include

  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • New options for PBSA calculations, including new solvers and dielectric models;
  • Updates to MMPBSA.py, including access through NAB of two new GB models;
  • New documentation and tools for inspecting and modifying Amber parameter files;



Comments

ADF2013 released

I just got an email from CCL highlighting the release of ADF2013.

SCM is proud to announce the 2013 release of the ADF modeling suite. We continue to improve and expand our software suite with the aid of our academic and industrial ADF authors and other partners. Several enhancements and new features have been implemented in our molecular Density Functional Theory (DFT) code ADF and its periodic DFT companion BAND. Our semi-empirical Density Functional based Tight-Binding (DFTB) module has been updated and we offer Dr. Stewart's latest MOPAC2012 module including the PM7 model. The parallelization of the reactive MD module ReaxFF from van Duin and co-workers has been improved considerably.

There is more information here

ADF

I also noted there is a free 30-day trial available

Fully functional versions of all modules of our 2013 release are available free of charge for a 30-day evaluation period. The programs may be run on any machine at your organization, with full support. Just fill out our Free Trial Form. Other questions? : e-mail us at info@scm.com.



Comments

GPU accelerated version of GROMACS 4.6

I thought I would give a plug to an upcoming webinar that Dr. Erik Lindhal at Stockholm University and NVIDIA are presenting to discuss latest GPU-acceleration technologies available to GROMACS users. Join to learn about latest accelerated version of GROMACS 4.6, which features are supported, it's installation and use, and how it performs with latest NVIDIA Kepler GPUs.   The webinar is planned for Thursday, April 4th, 2013 9:00 AM - 10:00 AM Pacific Standard Time

Register here: goo.gl/ioQMd

There is a list of GPU accelerated application here



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SAR Table updated

The SAR Table app has had the ability to match scaffolds to molecules for a while now, but as of the latest release (1.3.4) just submitted to the AppStore, it will be able to match more than one scaffold at once. The actual process of performing the scaffold match is provided by a webservice (molsync.com).

More details here.



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Smina

Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.



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Molecule Calculator

After I wrote the article about javascript based molecule viewers I’ve been sent a couple of links demonstrating their use. One particularly interesting one is MolCalc an online molecular calculator that uses JSmol to build and render structures.

molcalc1

Once the molecule has been built and minimised using the MMFF force field you can then use GAMESS to calculate a range of molecular properties.

molcalc2

MolCalc is distributed through GitHub under the GPL license github.com/jensengroup/molcalc. You must obtain a copy of the GAMESS code separately from www.msg.ameslab.gov/gamess/download.html Since this uses javascript for the interface it will work on mobile devices.



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Parallel Quantum Solutions

I’ve added Parallel Quantum Solutions to the alphabetical listings.

We estimate that well over 80% of CPU cycles spent in ab initio computations are used in optimizing geometries at the SCF or DFT levels,and in computing molecular properties, such as vibrational frequencies and NMR chemical shifts. Such calculations are extremely well suited for parallel implementation. Shifting them to an inexpensive and fast parallel machine can free up expensive workstations for more demanding calculations.




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SZMAP v1.1.1 Released

OpenEye have announced that SZMAP 1.1.1 has been released. This is a bug fix release that repairs one major bug and several minor ones.

  • A rare but important bug in how the SZMAP application decides which apo grid points will be analyzed under certain circumstances has been fixed.
  • The metadata added to SZMAP output now includes the correct version number.
  • The position of points tested for stabilization by GAMEPLAN no longer differ slightly between different architectures.
  • Running GAMEPLAN from a directory containing the word "gameplan" works properly now.
  • The GRID_COMP utility now generates the appropriate subset of probe orientations for displacement operations.
  • The Water Orientation VIDA Extension now clearly identifies ligand or protein displacement entries in the selection pop-up menu.
  • The WaterColor VIDA Extension no longer switches the hypothesis molecule to wireframe when run while a hypothesis is selected in the list window.

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding, giving insights into the role of water molecules in ligand binding. The included tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.

szmap



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Fen Zi GPU-based MD simulations

Fen Zi (yun dong de Fen Zi = Moving MOLECULES) is a CUDA code that enables large-scale, GPU-based MD simulations. The code of Fen Zi is now available in Google Code at http://code.google.com/p/fen-zi/. Any help or feedback is welcome!

Fen Zi currently includes: - NVT and NVE ensembles (NPT coming soon) - Force field: CHARMM force field, Flexible Water Models - Lennard-Jones interactions: Switching or shifting - Long distance electrostatic interactions: Ewald summation method and Reaction field - Solvent: Explicit or implicit model; TIP3; Flexible SPC/Fw water model - Exclusion lists for VDW and electrostatic interactions: NBXMod from 1 to 5 - Restraint potentials to probe the free energetic evaluation of processes - Shake/Rattle bond constraints for atom–atom bonds involving at least one hydrogen atom in the bonded pair

There is a listing of GPU accelerated scientific applications here.



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MacMolPlt Updated

MacMolPlt is a cross-platform (Mac OS X, Linux and Windows) gui for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties.

Surface

Version 7.4.4 update notes:

  • Fixed a seg fault when reading a single mode in a molplt file.
  • Fixed a bug related to fragement parsing.
  • Fixed a problem when deuterium was encountered. There is still not proper support for isotopes, but MacMolPlt should behave normally if they are encountered.
  • Modified MCSCF natural orbital parser for a recent change to GAMESS.
  • Added recent GAMESS coupled-cluster methods.
  • Added a parser for EOM-CC natural orbitals.
  • Added a parser for CAS-SCF diabatic molecular orbitals.
  • Cleaned up some potential 64 bit issues.



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Using ChemBioDraw with MOE

As I mentioned in my recent review of MOE 2012 there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package? Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL (scientific vector language) we can use ChemBioDraw as the external editor. Full details of the script are here.

gleevex

The Applescript section contains more tutorials, scripts and resources.


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A Review of MOE 2012

I’ve just finished a review of the latest version of MOE from the Chemical Computing Group.

There are a number of new features that will be of particular interest to Mac users and I’ve included a few tips for using Marvin as the external 2D chemical drawing package.

system2

There is a collection of software reviews here.


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Chemcomp release PSILO version 2012.11

The Chemical Computing Group have announced the release of PSILO version 2012.11. PSILO is a protein structure database and visualization system that provides an easily accessible, consolidated repository for macromolecular and protein-ligand information. Some key features in PSILO include:

  • 3D Interaction Query
  • Pocket Similarity Search
  • Project Standard Orientation

New and enhanced features in PSILO 2012.11 include: domain motif search, nonredundant BLAST summary report, automatic GPCR annotation and Interactive protein:ligand interaction diagrams. PSILO offers research organizations a means to systematically track, register and search both experimental and computational macromolecular data. A web-browser interface facilitates searching and accessing public and private data


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DIRAC 12 Released

New features in DIRAC12 (released 12/12/12) Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations

  • 2-component relativistic Effective Core Potentials (ECPs)
  • London Atomic Orbitals (LAOs) at the DFT level
  • Simple magnetic balance for NMR shieldings
  • LAO current densities
  • Overlap diagnostic for TD-DFT calculations of excitation energies
  • Pipek-Mezey localization by trust-region optimization
  • Long-range MP2/short-range DFT
  • Atomic start guess for SCF calculations
  • MP2 natural orbitals
  • Complex/Damped DFT response module
  • New Lanczos algorithm for relativistic Algebraic Diagrammatic Construction (ADC)


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MOE 2012.10 released

NEW & ENHANCED FEATURES IN MOE 2012.10

Integrated Protein Engineering Applications

  • Residue scanning to identify critical residues for affinity
  • Search for optimal mutations to modulate thermostability
  • Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer

Domain Motif Searching

  • Compare protein domains based on secondary structure elements
  • Search proteins for secondary structure sub-geometries
  • Identify similarities independent of sequence

Amber12:EHT: New Force Field for Biopolymers and Small Molecules

  • Amber12 parameters for proteins and nucleic acids
  • Extended Hückel Theory parameterization of small molecules
  • More precise treatment of resonance and substituent effects

Reaction-based Library Enumeration and Screening

  • New reaction engine combined with library enumeration or sampling
  • Sketch reactions or core/R-group libraries
  • Screen products with 2D or 3D filters (educts & products)

Usability Enhancements

  • Docked System Manager with control over surfaces
  • Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc.
  • 2D sketcher integration with MOE Window

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Molegro Virtual Docker

CLC bio is pleased to announce a new release of Molegro Virtual Docker , an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

New features in version 5.5:

  • A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.

  • We also added a new execution mode in the Docking Wizard: 'Run Docking in Multiple Processes'. This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used.

  • The ray-tracer has been improved to more closely match the live 3D view output. This makes it possible to create high resolution renderings of the 3D view.

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OpenEye Toolkits have been released

OpenEye is pleased to announce that the OpenEye Toolkits v2012.Oct have been released. This release includes the C++, Python, and .NET versions of the Toolkits

C++ examples build system changed to CMake for all supported platforms: Linux, Windows, and OSX.

This is a new release of the OpenEye Toolkits with versions of the following libraries:

OEChem TK:1.9.0
OEDepict TK:2.0.4
OEDocking TK:1.1.3
Grapheme TK:1.0.4
GraphSim TK:2.0.3
Grid TK:1.4.1
Lexichem TK:2.2.0
MolProp TK:2.1.4
Omega TK:2.5.0
Quacpac TK:1.6.0
Shape TK:1.8.3
Spicoli TK:1.1.3
Szybki TK:1.7.2
Zap TK:2.1.4

Details of the changes to the individual libraries are here

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More GPU accelerated applications

After posting about Lumo which accelerates the visualization of molecular orbitals from electronic structure calculations by harnessing the power of the gGPU, I received the following email which describes more GPU accelerated applications.

New Molecular Dynamics Benchmark Reports  Oct 2012 are now available to compare CPU vs GPU & NVIDIAs New Kepler GPU Performance.

These reports are intended to assist computational chemistry researchers and IT managers to discover acceleration achieved by running MD applications on GPU based computing solutions.

Download Benchmark Reports - www.nvidia.com/GPUTestDrive

AMBER, GROMACS, LAMMPS, NAMD reports provide: a.      Benchmark data on latest GPU architectures b.      Hardware recommendations

Also, if you are looking to try GPUs: Sign up for a FREE GPU Test Drive on a remote cluster with AMBER, GROMACS, LAMMPS and NAMD preinstalled - www.nvidia.com/GPUTestDrive

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Lumo:- Molecular Orbital Visualisation

I’ve recently noticed an increasing interest in harnessing the computational power of the graphics card to accelerate scientfic calculations.

The latest application is Lumo which accelerates the visualization of molecular orbitals from electronic structure calculations by harnessing the power of the graphics processing unit in modern macs. Lumo currently reads formatted checkpoint calculations from Gaussian03/09 calculations and there is preliminary support for Orca output files. Lumo was designed to speed up the slow part of looking at molecular orbitals and making molecular orbital diagrams. Lumo eliminates several steps along the process by reading in the output of programs like Gaussian, quickly visualizing the orbitals, and creating pictures of the essential orbitals in seconds.

Lumo requires Mac OS 10.6 or higher, 64-bit processor, and an OpenCL capable compute device. Lumo is routinely run on MacBook Pros and MacBook Airs. For analysis of larger systems, it is recommended to have at least 4GB of system RAM.

There is a movie of Lumo in action on the website

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Viewing Docking results in Vortex using Astex Viewer

I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.

I’ve been working with Mike Hartshorn and the people at Dotmatics who have incorporated OpenAstexViewer (a 3D molecule viewer) into the application you can read the full article here..

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Review of ForgeV10

This is a review of ForgeV10 the latest offering from Cresset, whilst a new product those familiar with FieldAlign and FieldTemplater will recognise much of the functionality. ForgeV10 allows the scientist to use Cresset’s proprietary electrostatic and physicochemical fields to align, score and compare diverse molecules. It allows the user to build field based pharmacophores to understand structure activity and then use the template to undertake a virtual screen to identify novel scaffolds.

There is a compilation of software reviews here.

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MOPAC12 released

MOPAC12 A practical quantum chemistry tool for modeling biological systems and co-crystals. MOPAC2012™ brings major improvements in the prediction of intermolecular interactions and hydrogen-bonding. This significantly improves geometries and energies of proteins, crystals, co-crystals, metal clusters, inorganics and other condensed phase systems. New PM7 method significantly improves intermolecular energies, providing increased accuracy for condensed phase chemistry.  PM7 can be applied to modeling enzyme reactions and predicting co-crystals.

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SZMAP updated

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.

NEW FEATURES

  • The Water Orientation VIDA Extension has been completely rewritten to be easier to use and more feature-rich, making it simple to find key waters and understand their interactions. Each water site can be labeled by its energy, van der Waals energy, and degree of order. The 3D representation shows whether a site is disordered, an acceptor, a donor, or both. Individual waters can be exported for use elsewhere. The other extensions have also been improved.
  • A new command-line program called GAMEPLAN has been released. GAMEPLAN runs several quick SZMAP calculations and analyzes the results to examine how the existing ligand chemistry aligns with the pocket environment. It also produces hypotheses of ligand modifications to improve its affinity, based on the energetics of the water environment directly adjacent to the ligand.
  • SZMAP output has been simplified: sections are clearly identified, the water orientation data is less obtrusive, and an updated set of grids is produced (neutral difference free energy, van der Waals, order, and mask). The Watercolor VIDA Extension now sets contour levels to emphasize significant results.
  • The speed of SZMAP stabilization calculations for both grids and arbitrary coordinates has been increased. Results from an existing apo protein calculation can be re-used, speeding up calculations for a series of compounds and/or poses in a single binding site. The speed of stabilization calculations is improved by avoiding extra calculations on the isolated ligand.
  • It is now easy to produce SZMAP results for just the region in the apo pocket where water has been displaced by the bound ligand, clarifying the analysis of water in the apo protein.
  • The programs SZMAP and GAMEPLAN will check to make sure input files contain partial charges and explicit hydrogens to avoid wasting time on meaningless calculations when the input is incorrect.
  • Protein preparation is easier because PCH (which adds partial charges to molecules and separates protein from ligand) now provides more control over the process and can work around structures that contain unsupported elements. PCH can now split out waters into a separate file.

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Added Quantum Expressoto alphabetical listings

Quantum Expresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Details of the packages is available in the documentation

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New tools from COSMOLOGIC

Two brand new tools from COSMOlogic which might be of greater interest for all those working in drug design:

1) COSMOsim3D Based on an idea of Michael Thormann (Origenis) we have implemented COSMOsim3D as a very efficient method for alignment and 3D similarity using local sigma profiles, i.e. local histograms of the COSMO sigma surface on a 3D grid. By that molecules get aligned in a way that maximum similarity of the sigma surfaces is achieved. In a paper which has just got online in JCIM (see http://pubs.acs.org/doi/abs/10.1021/ci300205p) we demonstrate the extraordinary performance of this method for bioisoster search and drug activity class enrichment.

2) COSMOsar3D According to COSMO-RS theory, which is widely validated in fluid phase thermodynamics, the final grid of local sigma profiles produced at the end of a COSMOsim3D alignment of ligands should represent a complete set of descriptors for molecular interactions. Furthermore it can be shown that with these descriptors the free energy of binding of a ligand in a receptor should be a linear function of the descriptors, and thus be optimally suited for the PLS analysis usally applied in molecular field analysis. Therefore we implemented the COSMOsar3D method a new variant of the traditional comparative field analysis, know as CoMFA. And indeed, testing this idea on the Sutherland data set we could show that it outperforms the seven reported 3D-QSAR methods tested therein not only with respect to prediction accuracy, but also with respect to robustness with respect to grid position, grid size, and small misalignments of the ligands. (see http://pubs.acs.org/doi/abs/10.1021/ci30 0231t)

Everybody who likes to test these two methods on his datasets is invited to do this based on a free evaluation license. You can use the tools either stand alone, or integrated in the Open3DQSAR software (http://open3dqsar.sourceforge.net/)

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Cresset Product Update

I was at the Cresset Science Meeting last week and heard about the plans to update their comprehensive suit of drug discovery and design computational tools.

Together with an interesting updates to the tools the suite has undergone something of a makeover, all of the software tools have be renamed using a “Fire” theme and refocussed to specific users needs rather than the software capabilities. The renaming will not be complete until September so in the interim the links on some of the download pages still point to the originally named application.

TorchV10lite is a free 3D molecule viewing, editing and drawing application that shows your molecules in 3D overlaid with field patterns generated using their proprietary field technology together with 2D structure and physicochemical properties. It is the replacement of FieldView.

TorchV10 is a powerful design and 3D SAR tool for medicinal chemists. It is used to take leaps in structural design by identifying compounds with similar fields but different 2D chemical structures while maintaining or improving biological activity. It is the replacement for FieldAlign and due for release very soon.

SparkV10 is a powerful way of generating novel and diverse structures for your project.  sparkV10 uses Cresset’s field technology to find biologically equivalent replacements for key moieties in your molecule, enabling you to find new structures in new chemical space. You can then use calculated physiochemical properties to filter and select the best designs. sparkV10 is the exciting replacement for FieldStere and due for release very soon.

The three applications above look to be intended for use by Medicinal Chemists whilst the remaining two applications are perhaps better suited to those more experienced in computational chemistry.

ForgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint, using the shape and electrostatic character of your molecules to create qualitative and quantitative 3D models of activity. forgeV10 combines FieldAlign and FieldTemplater in a single application,

BlazeV10 uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar shape and electrostatic properties. It is installed and runs on a Linux cluster but is operated through a web-browser, enabling access from any platform and multiple locations.

Many molecular visualisation/modelling tools seem to assume the charge associated with an atom sits as a point at the centre of the nucleus, whilst this makes the computation easy it does not really reflect what the electrostatic surface really “looks like”. Cresset has pioneered the use of field point descriptors to give a more accurate description of the charge around an atom and to enable better comparisons and visualisation. This has been shown to be particularly important when trying to understand some molecular interactions such as Aryl-Aryl interactions or creating bioisosteric replacements.

HeteroFields

Cresset now have an impressive suite of tools for drug discovery and I hope to review them in due course.

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Computational Chemistry Competition

As part of an initiative to provide computational chemistry tutorials there is a competition now on.

Website is here.

Details for the competition Requirements Use freely available software tools and develop tutorials & models for workflows as requested in the challenges. Criteria to Judge

  • Quality of predictive models
  • Statistical measures, held-out test sets
  • Quality of workflows
  • Are these state-of-the-art?
  • Clarity of the tutorials
  • Suitable for undergraduate courses
  • Include principles of underlying science
  • Include description of “common pitfalls”
  • Include description of all preparative steps & required resource
  • Ease of use of the tools
  • Can they be tailored/amended if new insights emerge (project specific or general insights)?
  • Innovation of the computational methods

Challenges

  • Challenge 1: Workflow to analyze HTS data & build models for further hit finding
  • Challenge 2: Structure-based design workflow, new chemotypes
  • Challenge 3: Structure-based design workflow, medicinal chemistry strategy
  • Challenge 4: Call for innovative drug discovery workflows

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FMCS 1.0 - Find Maximum Common Substructure

Andrew Dalke has just released fmcs-1.0. It finds a maximum common substructure of two or more structures. Some of the features are:

  • handles 1,000s of structures
  • several different atom and bond comparison schemes
  • modifiers to require ring bonds only match ring bonds, or that incomplete rings are not allowed in the MCS
  • user-defined atom class typing through isotope labels (SMILES) or through an SD tag field
  • uses an exact solution to find a maximum common substructure
  • eports the current best solution if the timeout is reached

The software is distributed under the 2-clause BSD license and available for no charge from https://bitbucket.org/dalke/fmcs/downloads/fmcs-1.0.tar.gz

You must have the Python bindings to RDKit in order to run fmcs.

Usage details are in the README, shown also in the project page at:  https://bitbucket.org/dalke/fmcs/

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Crystal09 updated in alphabetical listing

Just noticed the website is open and available for registration.

CRYSTAL is a general-purpose program for the study of crystalline solids

New features

  • Static polarizability and dielectric tensor through a Coupled Perturbed HF/KS scheme
  • Phonon dispersion using a direct approach and infrared intensities through a Berry phase approach
  • Transition state search
  • Constant pressure geometry optimization of cell constants and atomic positions
  • Automated calculation of the elastic tensor of crystalline systems
  • Automated E vs V calculation for equation of state
  • New GGA functionals for solids
  • London-type empirical correction for dispersion interactions (Grimme scheme)
  • Automatic generation of nanotubes from single-layer systems
  • Helical symmetry for polymers
  • New tools for initial guess of SCF for d- and f-partly occupied atoms
  • New tools for the treatment of solid solutions
  • Revised implementation of Electron Momentum Density analysis and Compton profiles
  • Enhanced Massive-parallel version (MPPcrystal - distributed memory)

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forgeV10

forgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint

It is designed to

  • Decipher complex SAR and communicate the results
  • Design better molecules based on predictions you can trust
  • Prepare detailed pharmacophores
  • Virtually screen 10 000 compounds on your desktop
  • Generate ADME and off target activity profiles.

fieldalign_example_small

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Wolfram SystemModeler released

Stephen Wolfram has announced Wolfram SystemModeler on his blog.

SystemModeler is a very general environment that handles modeling of systems with mechanical, electrical, thermal, chemical, biological, and other components, as well as combinations of different types of components. It’s based—like Mathematica—on the very general idea of representing everything in symbolic form.

sysmodeler

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New Additions to alphabetical listings

Added to alphabetical listing

ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.

Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.

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OEDocking v3 released

OpenEye has to announced the release of OEDocking v3.0.0. OEDocking is a suite of well-validated molecular docking applications (FRED, HYBRID, POSIT) and their associated workflows. This release features the official introduction of HYBRID, as well as a major upgrade to FRED.

POSIT - Ligand guided pose prediction FRED - Fast exhaustive docking HYBRID - Ligand guided docking

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Graphite - LifeExplorer

Just added to the alphabetical listing

Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.

You can see a it in action here

http://www.youtube.com/watch?feature=player_embedded&v=9db1hXZARoo

Comments

Chemkit added to alphabetical listing

Chemkit is an open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.

Chemkit-builder1

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CFOUR added to the alphabetical listing

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. Studies of excited electronic states and other "multireference" problems are possible using the equation-of-motion (EOM) coupled-cluster techniques. These techniques which are closely related to (and in some cases identical to) so-called Fock space multireference coupled-cluster theory, offer a powerful means to study open-shell systems and decided advantages when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. Analytic derivatives are available for these methods. A number of methodological developments have been added to the program in the last two decades. These include: analytic second derivatives for all coupled-cluster approaches up to full CCSDT; the calculation of NMR chemical shifts at MP and CC levels of theory; the calculation of anharmonic force fields (via numerical differentation of analytic derivatives); relativistic corrections; corrections to the Born-Oppenheimer approximation at the CC level; nonadiabatic coupling within the EOM framework, and several others.

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SchroŐądinger Suite 2012 supports Mac OS X

It was recently announced that the Schrödinger Suite 2012 now supports Mac OS X, I don’t have many details other than those on the website. There is now a Mac OS X native version of Maestro 9.3, and PyMOL 1.5 supports Mac OSX 10.7, there is encrypted file transfer channel to clusters, including the Cloud (Linux and Mac only). There is also a Mac OS X native version of Canvas 1.5.

If anyone has more information please let me know.

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AMBER 12 released

A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-

  • Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
  • Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
  • An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
  • Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • Simplified installation and automatic update support.
  • Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
  • More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.

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SYBYL-X 2.0 release now available

SYBYL-X 2.0 release now available - with new Molecular Data Explorer, QSAR enhancements, and updates for Surflex-Sim and Surflex-Dock to make performing your CADD modeling studies more intuitive and efficient.   

The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days.

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Stardrop Review

I’ve just posted a review of Stardrop an application from Optibrium that is designed to aid decision making for scientists involved in drug discovery.

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Scripting Vortex 8 molecular shape matching

One of the critical activities of most drug discovery programs is the identification of novel leads, these hits can come from high throughput screening or fragment-based screening There is however great interest in virtual screening which allows the evaluation in silico of a vast number of compounds and the selection of a subset that have a greater chance of desired activity. The virtual screening can be achieved by searching using sub-structures or molecular descriptors, by docking potential ligands into the target protein and scoring the resulting docked pose, or by comparing with the shape and/or electrostatic map of a known ligand.

Shape-it is a tool developed by Silicos-it that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of Gaussian volumes as descriptor for molecular shape as it was introduced by Grant, J.A.; Gallardo, M.A.; Pickup, B.T. (1996) ‘A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape’,J. Comp. Chem. 17, 1653-1666.

This script shows how to run shape-it from within Vortex, bringing in the shape matching scores for filtering and analysis.

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New applications added to alphabetical listing

Open3DALIGN is a command-line molecular alignment tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.

Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script).

Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields.

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ICM Update

MolSoft have announced the release of ICM version 3.7-2c.

New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).

The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.

Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).

Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.

"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)

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RESP ESP charge Derive version III.5

I just got this message.

I am pleased to announce the release of the program RESP ESP charge Derive version III.5 (or R.E.D. III.5) and its related tools (Ante_R.E.D.-1.5 and X R.E.D. III.5) available @ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning, - Update of the Mini-HowTo & Tutorials, - Better handling of Gaussian, GAMESS and Firefly error messages, - Charge value rounding off errors automatically corrected at 10-6 up to 10-2 depending on the user choice, - Handling geometrical constraints in the P2N file format (geometry optimization using the Gaussian program), - Two new scripts for data submission in R.E.DD.B., - New version for the RESP program: version 2.2 with updated documentation. The R.E.D. III.5 tools are distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. tools is available @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/. News about the latest developments of R.E.D. IV can be found @ http://q4md-forcefieldtools.org/RED/popup/news.php. Best regards, The q4md force field tools team

R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.

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Silicos-it tools

I’ve mentioned Silicos-it in the past and I thought I’d highlight them again since they have had a major makeover, the website has moved and the tools have been updated and renamed.

Silicos-it has contributed it’s expertise to the chemoinformatics community by porting its source code into the open source domain. Examples include the spectrophore descriptors, the filtering program filter-it and the pharmacophore tool align-it.

Command-line tools

Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.

I used the filter-it (previously called Sieve) in a Vortex script, I’ve rewritten the script and the tutorial to account for the name change.

Strip-it™ is a tool to extract molecular scaffolds according predefined rules. These rules are based on the definitions of scaffolds as described by Bemis & Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).

Align-it™ is a pharmacophore-based tool to align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment.

Shape-it™ is a shape-based alignment tool by representing molecules as a set of atomic Gaussians. The software is based on the method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).

Spectrophores are one-dimensional descriptors generated from the property fields surrounding the molecules. This technology allows the accurate description of molecules in terms of their surface properties or fields. Comparison of molecules’ property fields provides a robust structure-independent method of aligning actives from different chemical classes. When applied to molecules such as ligands and drugs, Spectrophores can be used as powerful molecular descriptors in the fields of chemoinformatics, virtual screening, and QSAR modeling. The Spectrophore code was developed by Silicos, and donated to the OpenBabel project in July 2010.

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Perspectives on the state and future of Computer aided molecular design

I just thought I’d mention that Journal of Computer-Aided Molecular Design commissioned some Perspectives on the state and future of the field to commemorate the journal's 25th anniversary and have made this content open access for a limited period.

Special Issue: The next 25 years: Commemorating the 25th anniversary of the Journal of Computer-Aided Molecular Design

There are some very interesting insights, well worth reading.

Edit

Have a read of Alpha shock by Mark A. Murcko • W. Patrick Walters

Sanjay toggled the telepresence feature on his iPhone (standard since IOS 27.2) and he and Paolo were instantly ‘‘together’’ examining a set of images from the virtual pharmacology study.

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OMEGA updated

OMEGA v2.4.6 has been released. This is a major release with new features including an extension to the MMFF94 force field for three coordinated boron compounds. Designed for use with the large libraries required for computer-aided drug design, OMEGA rapidly generates multi-conformer structure databases.

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DivCon Discovery Suite Updated

QuantumBio Inc. have announced the release of Version 5.1.1 of its DivCon Discovery Suite which includes support for the newest version of the Molecular Operating Environment (MOE) platform from Chemical Computing Group, Inc.

MOE/DivCon GUI is an integration interface that joins the QBLib with the powerful Molecular Operating Environment (MOE) from the Chemical Computing Group (CCG), creating a technological innovation for protein/ligand scoring (energetically favorable), featuring QM, PWD, and NMR Scores.

The update also includes:-

  • MOE/DivCon: For pairwise energy decomposition heatmap, sequence alignment within the MOE/DivCon interface has been completely overhauled in order to use CCG's sequence alignment tool.
  • MOE/DivCon: Multitasking within the MOE/DivCon graphical user interface runs freely while DivCon is running in the background. Improved QM convergence reporting to MOE's svl window.
  • File Processing: Included HDFView and QBReporter applications for opening and processing *.h5 output files, and translating them to Excel or OpenOffice spreadsheet files. Reported results include QMScores, partial charges, gradients, and significant events. QBReporter requires that OpenOffice 3.3.0 or greater from OpenOffice.org has been installed and that the resulting soffice executable is available within the command line $PATH.
  • Core: Support for Sun Grid Engine (SGE) in addition to the Portable Batch System (PBS). Note: SGE requires that its parallel environment (PE) be activated in order to run multiprocessing jobs.
  • Core: Shipment of both 32bit and 64bit native versions of all Linux binaries in order to account for larger memory, disk, etc (and therefore larger target/ligand structures).
  • Core: Separation of QuantumBio-specific software from 3rd party binaries (such as mpirun) in order to allow for parallel installations of the same.
  • MOE/DivCon: Inclusion of ${QBHOME}/bin/qbmoe and ${QBHOME}/bin/qbmoebatch to run system-installed MOE and MOE/batch with QuantumBio-required options.
  • MOE/DivCon: Addition of support for MS Windows7 (64bit) both for preparation and analysis. Prepared structures can then be characterized with qbmoebatch on Linux or Mac OS X.
  • Documentation: Completely updated on-line documentation for MOE/DivCon.
  • MOE/DivCon: Entirely redesigned and streamlined dialogs, and improved integration with standard MOE structure preparation and analysis tools.
  • MOE/DivCon: Patented QMScore integrated as an available score function for MOE tools including Dock, Scaffold Replacement, BREED, etc.
  • DivCon: Support for additional input file formats including cif, sdf, and h5.
  • DivCon: Command line --help switch improved to provide default settings, simplified

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Q-Chem Updated

I just got this message:-

We are pleased to announce the official release of Q-Chem 4.0.  Q-Chem 4.0 represents the latest development in quantum chemistry methodology and includes:

  • Dispersion-corrected and double hybrid DFT functionals;
  • Faster algorithms for DFT, HF and coupled-cluster calculations;
  • Structures and vibrations of excited states with TD-DFT;
  • Methods for mapping complicated potential energy surfaces;
  • Efficient valence space models for strong correlation;
  • More choices for excited states, solvation and charge-transfer;
  • Effective Fragment Potential and QM/MM for large systems;
  • Shared-memory for multicores and implementations for GPU's.

A complete list of the new features can be found at the our website: http://www.q-chem.com.

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NWChem 6.1 and ADF2012 released

The updates to two of major packages for computational chemistry have been announced

NWChem 6.1 has been released with the latest Global Arrays Toolkit (GA-5.1). Full details of the update can be found here.

SCM has announced the 2012 release of its suite of chemical modelling programs: ADF, BAND, DFTB, MOPAC, ReaxFF, and COSMO-RS. Full details of the update can be found here.

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ORCA 2.9 version available

ORCA is a modern electronic structure program package has been updated

New Features

1) The parallelization of the program is now completed. All modules, including MRCI, are now parallel. Parallel performance has been improved in numerous cases. 

2) A new module for performing efficient spin adpted single excitation configuration interaction calculations for open shell systems (ROCIS). This is particularly powerful for the calculation of transition metal L-edge X-ray absorption spectra. It is parallelized

3) A new module performing molecular dynamics calculations with ORCA. Also available for methods that only feature numerical gradients. 

4) MDCI module: • Orbital optimized coupled cluster version for RHF and UHF (also parallelized) • Brückner coupled cluster (including triples) for RHF and UHF • SEIO functional for orbital invariant, stationary coupled pair calculations • Open shell LPNO-CEPA,QCISD and CCSD methods • Parameterized CCSD (pCCSD) in canonical and LPNO versions (RHF and UHF)

5) CASSCF: • Relativistic CASSCF for the variational treatment of spin orbit coupling. Also uses symmetry. • Projection SOC states on spin-free states possible • Kramers restricted RELCAS • Numerous improvements in NEVPT2 (COSMO, Trajectories and scans, Direct-RI modeless storage) • Improved convergence and convergence aids (... but we are still working on this) • Spin-Spin coupling in QDPT CASSCF/NEVPT2 for magnetic properties • Determinant based full CI program added for the CI step

6) MRCI • Fully parallelized including the QDPT procedure for magnetic properties

7) General/Misc. improvements • VDW10. Latest dispersion correction from the group of Grimme • Nonlocal DFT-NL for incorporation of dispersion in DFT • PW6 B95, PWP B95, RI-PWP B95 functionals • Rappoport/Furche optimized basis sets for properties • Basis set extrapolation now works also with def2 basis sets • Densities for interactive orcaplot • Differences and transition densities in orcaplot • Natural orbitals for unrelaxed MP2 density • SOS-MP2, SOS-RI-MP2, SOS-OO-RI-MP2 energies + gradients • DKH picture change for g-tensors • Overlap fitted RIJCOSX procedure leads to further speedups and improvements in accuracy • Libint2 for more efficient integral evaluation (uses contraction) • Parallelization of point charge correction for QM/MM • Interface to the MRCC program by Mihály Kállay

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Scripting Vortex

This is the fourth tutorial on scripting Vortex a chemically intelligent data visualisation package. In the previous tutorials we have looked at getting data from OpenBabel, sieve, and cxcalc in this tutorial we will be using MOE as the compute engine. MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means by which many users will interact with the program it is worth finding out about the command-line tools that are available. These tools are often accessed by pipeline tools such as Knime to allow rapid processing of large files. CCG provides four very useful command-line tools in particular sddesc allows the calculation of some or all of the MOE molecular descriptors for each molecular entry.

The Vortex Scripts

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE

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Molecular FORECASTER

I just heard about a platform - FORECASTER - that includes programs for drug discovery and process chemistry, these include

  1. FITTED, a docking program
  2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
  3. CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
  4. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
  5. REDUCE, a program that filters using descriptors and functionnal groups
  6. REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
  7. IMPACTS, a sites of metabolism prediction program (CYP 450)
  8. ACE, a program that predicts the stereochemical outcome of reactions

All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows. 

You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery

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MOE 2011 Review

I’ve just added a review of the latest version of MOE from Chemical Computing Group.

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MOE 2011.10 released, Lion compatible

CCG have announced the release of MOE 2011.10. This includes a new license manager compatible with LIon.

Some of the new and enhanced features in MOE include:

================================================================

Non-Bonded Interaction Visualization Model - Visualize halogen bonds, H-bonds, CH-X, proton- for interactive modeling - Calculate strengths using Extended Hckel Model - Display strengths and interactions in 2D Ligand Interaction Diagrams Sequence Editor Redesign - Wrapped view, zoom, chain name/tag, etc. - Synchronized coloring (% identity, similarity, Clustal X, RMSD) - Cut and paste for loop grafting, inserting linkers, filling gaps, etc. Combinatorial Build in Pocket - Add R-groups to one or more attachment points in 3D pocket - Apply 2D and 3D filters, refine in (flexible) pocket and score - Use Builder to scan fragments for interactive ligand optimization Analysis of Solvent in Binding - Calculate within minutes a solvent binding free energy map using 3D-RISM - Calculate water, salt and hydrophobe solvation densities in complex or apo receptor - Diagnose how well alternate groups take advantage of water upon binding Macromolecular System Preparation - Correct common problems in protein structures automatically - Browse alternate conformations, cap termini, build missing loops - Optimize hydrogen bond network by flipping residues and adjusting states GPCR Family Database and Alignment Tools - Identify and annotate transmembrane regions of GPCRs - Add alignment constraints to improve GPCR sequence alignments - Augment a database of GPCR crystal structures with in-house data


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New major release of Molegro Virtual Docker

Molegro is pleased to announce a new major release of Molegro Virtual Docker, an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

Major new features in version 5.0: -GPU-accelerated docking on CUDA supported hardware making it possible to screen drug-like compounds up to 30 times faster than using conventional CPU-based methods. The GPU implementation builds upon and extends the research described in the paper "GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution" (http://dl.acm.org/citation.cfm?id=2001576.2001818). -The new 2D Ligand Map provides an easy way to inspect and visualize protein-ligand interactions.

For more information, or to download a trial version, please visit our company website at: http://www.molegro.com


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Molegro Virtual Grid

Molegro Virtual Grid creates an infrastructure for distributing docking runs on multiple machines. By simply installing the MVG agent on a computer, its resources can be used transparently by the grid controller. Virtual Grid support is built into Molegro Virtual Docker: for instance, to dock a library of compounds against a receptor, simply setup a compound data source, and select 'start job on Virtual Grid' in the Docking Wizard. Molegro Virtual Grid is multi-core aware and can be installed on any platform: Linux, Windows, and Mac. The machines in the grid do not need to run the same operating system. Now added to the alphabetical listing

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Release of FieldStere V3.0

Cresset have announced the release of a new version of popular bioisostere replacement tool, FieldStere.  FieldStere is a fast and powerful software tool which uses Cresset’s innovative field-point technology, together with a database of molecular fragments, to help guide drug discovery projects and generate new intellectual property.  Version 3.0 includes impressive updates to the science and user interface, and constitutes the most significant scientific update to FieldStere since its introduction.

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Scripting Vortex

Read More...
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Gaussian pages updated

Gaussian pages updated Read More...
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Amber on GPU

Amber usage survey Read More...
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FieldTemplater released on the Mac

FieldTemplater released on the Mac Read More...
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WebMO version 12 released

WebMO version 12.0 has been officially released Read More...
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Turbomole Updated

TURBOMOLE:  New Release 6.3 Read More...
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FieldAlign updated

Cresset announced the release of FieldAlign 3.0.1. Read More...
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QuantumBio Inc. and Chemical Computing Group, Inc. Announce the Release of the DivCon Discovery Suite for the Molecular Operating Environment (MOE)

 QuantumBio Inc., a leader in Structure-based and Fragment-based Drug Discovery solutions, based upon their next-generation linear-scaling quantum mechanics (QM) methods, has announced the release of DivCon Discovery Suite 5.0 for the Molecular Operating Environment (MOE) platform Read More...
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silicos tools for Drug Discovery

silicos tools for Drug Discovery Read More...
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iBabel

Here is the latest version of iBabel (3beta3), Read More...
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FieldAlign Review

You can read the FieldAlign Review here.
Read More...
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Gabedit updated

The latest release 2.3.5 of Gabedit is now available Read More...
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Review of FieldView

A review of FieldView. Read More...
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Review of MOE 2010.10

Read More...
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MOE Update

Chemical Computing Group have announced that MOE 2010.10 will be sent out on the first week of December Read More...
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CompChem tools

Useful tools for chemists (Linux/Mac OSX available). Read More...
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MOPAC2009 Updated

MOPAC2009 updated October 2010 Read More...
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QuantumBio

Integration of a quantum mechanics package with MOE Read More...
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Added Theseus

Added Theseus to the alphabetical listing Read More...
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FieldView is now available for MacOSX

Some time ago Cresset asked about interest in porting FieldView to Mac OSX, well I’m delighted to report that they have just announced that FieldView is now available for Mac OS X. FieldView is a molecular viewer/editor that is designed to show molecules with their associated Field patterns and physicochemical properties. Many molecular visualization/modelling tools seem to assume the charge associated with an atom sits as a point at the center of the nucleus, whilst this makes the computation easy it does not really reflect what the electrostatic surface really “looks like”. Cresset have pioneered the use of field point descriptors to give a more accurate description of the charge around an atom and to enable better comparisons and visualization. This has been shown to be particularly important when trying to understand some molecular interactions such as Aryl-Aryl interactions.
FieldView provides a richer more informative view of how molecules are likely to behave in biological systems. 
FieldView enables you to load your structures from SDF and MOL2 files as well as showing results from all Cresset applications. You can import and compare up to 10,000 compounds at once or copy and paste them into FieldView from your favourite drawing package.
Using FieldView you will be able to:
  • Create and modify structures using the in-built molecular editor
  • Automatically convert structures from 2D to a minimized 3D conformation
  • Clone and compare molecules side by side or overlaid using Cresset's unique Field technology
  • Understand how a compound’s activity, ADME and toxicity properties vary with their molecular Fields
  • View virtual screening results, such as those from FieldScreen, comparing 2D structures with a 3D overlay showing all the Fields of every ligand
  • Filter molecules based on the exact mix of properties you need
FieldView is available as a free download - to get your copy, simply fill out the registration form and they will send you a download link.
It is excellent we now have FieldView available on the Mac platform, I’d urge all chemists or biologists to download it and give it a trial.

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ICM_Browser Updated

Molsoft have announced the update of their free ICM-Browser. Read More...
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DIRAC10 Released

DIRAC, a Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations, the DIRAC program computes molecular properties using relativistic quantum chemical methods. Yesterday the release of DIRAC10 was announced with support for the following platforms Linux, AIX, Silicon Graphics, Apple under OS X (10.2 and higher), Sun Solaris, HP, Dec Alpha Read More...
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Molegro Virtual Docker Updated

Molegro is pleased to announce a new release of Molegro Virtual Docker, Read More...
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ADF2010 released

ADF2010 released Read More...
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NWChem Updated

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. Read More...
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CylView

Added Cylview a molecular viewer written in Python. Read More...
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MayaChemTools Update

MayaChemTools has been updated. Read More...
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Avogadro 1.0.1

Avogadro 1.0.1 available Read More...
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Aten Updated

Aten has been updated to version 1.5 Read More...
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Amber tools 1.4

AmberTools 1.4 is now available! Read More...
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AMBER 11 has been released

AMBER 11 has been released Read More...
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VASP Tools

Tools for VASP users Read More...
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APBS 1.2.1 has been released

APBS 1.2.1 has been released.  This is a bugfix release specifically aimed at addressing a problem with certain nonlinear Poisson-Boltzmann calculations. Read More...
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Added Libint

Libint:- Functions to compute two body integrals Read More...
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Latest iBabel Update

I’ve just released the latest version of iBabel (2.6) Read More...
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Installing Molden

Step by step instructions for downloading and installing molden. Read More...
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Gabedit added

Added Gabedit a graphical user interface to computational chemistry packages to the list of applications Read More...
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