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

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

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

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.

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.

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.

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.

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.

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.

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.

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)

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.

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.

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.

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.

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

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.

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.

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

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

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

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

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

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

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

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.

• I’ve just added a brief review of the latest version of MOE.

• 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