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;

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

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.

When you compare the amount of resources and effort that goes into computer games with the amount that is available for scientific software it is clear that the games industry wind hands down. It is not surprising therefore that some enterprising scientists are looking at leveraging games technologies to build new applications.

You can read more here Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists?

For an example application have a look at:-

UnityMol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. It was developed by Marc Baaden's team at the LBT laboratory at the IBPC institute of CNRS in Paris. UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). UnityMol can currently read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX potential maps and Wavefront OBJ meshes.

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.

OpenMM has been Updated

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.

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.

This might be of interest.

Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop.

Where:  Stanford University When:   March 26-29, 2013 Registration:  Free but required and spaces are limited. To register or for more information, visit http://simbios.stanford.edu/MDWorkshop.htm.

OpenMM (http://simtk.org/home/openmm) is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs).  Its performance, openness, and extreme flexibility  via custom forces and integrators  make it truly unique among simulation codes.

A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs.

The workshop offers two tracks:  one for those who want to use OpenMM to run molecular dynamics simulations (no programming experience is needed), and another for programmers interested in integrating OpenMM into their own software.  

The last two days of the workshop are devoted to having the OpenMM team assist participants with their individual projects.   You can sign up for an instructional track, just the open working days, or both.  

OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu.

[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs.  conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872.

[2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.

There is a listing of GPU accelerated scientific applications here.

UCSF Chimera Version 1.7 has been released. UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

New Tools:

• APBS (Surface/Binding Analysis) — interface to Poisson-Boltzmann electrostatics calculations with APBS, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
• AutoDock Vina (Surface/Binding Analysis) — interface to single-ligand docking with AutoDock Vina, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
• Model/Refine Loops (Structure Editing) — interface to Modeller for building missing parts or refining existing parts (the former Model Loops tool only performed the latter and did not facilitate combining the refined and unchanged parts)
• Notepad (Utilities) — allows entering descriptive text that can be saved along with sessions
• PDB2PQR (Structure Editing) — interface to structure cleanup and charge/radius assignment with PDB2PQR, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy

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.

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.

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.

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.

DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring.

The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids.  Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues.

The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket.

In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies.

Full information on what is new in DOCK 6.6

I use Moe for molecular modeling work, this uses a license.dat file in each installed MOE root directory that must be updated with the contents that you have been given by CCG (either by hard copy or e-mail). You can use any ASCII text editor (I used BBEdit) to edit the file. The FlexLM license manager lmgrd must be configured and run. Usually this runs quietly in the background and needs little intervention, however I've found that on some occasions the server quits (perhaps after updates) and needs to be restarted. However since it is something I don't need to do regularly I always spend a while working out the exact syntax. So I created this short Applescript to restart the server. Each time MOE gets updated you need to change the folder path, and I’ve updated the details to reflect this.

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.

The Applescript section contains more tutorials, scripts and resources.

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.

There is a collection of software reviews here.

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

A great collection of freeware tools provided by 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)
• 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)

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.

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

MolSoft have also released a new version of the free desktop molecular viewer ICM-Browser and the ActiveICM plugin  for viewing fully interactive molecules in web browsers.

Cresset have announced the formal release of sparkV10 the replacement for FieldStere.

• Updated molecular mechanics force field that uses a single analogue nitrogen atom and updates the field patterns for many functional groups including aromatic halides
• Added capability to read protein excluded volumes from pdb files
• Added new cluster algorithms for clustering of results
• Added option to edit reference molecules in the molecular editor
• Added capability to manage columns in the results table
• New optional module for scoring results using StarDrop models, this does not require access to a StarDrop server, simply place StarDrop model files in a directory and they automatically get used if you have the right  license.  The standard ADMET models that Optibrium have created are supplied but it works equally well with any models created by StarDrop.
• Added fragment import option in database generator
• Added capability to rescore all results against a 3D QSAR model using Forge or Torch
• Added capability to search databases for a particular fragment or substructure
• Added option to delete entire clusters from results
• Added depth cue to 3D window
• Added a GUI interface for selecting a portion of a molecule and writing command line arguments
• Cleaner GUI with improved buttons

Users should note:-

SparkV10 completely replaces Cresset’s previous “FieldStere” application. If FieldStere is currently installed then it is recommended to uninstall the binary to avoid confusion over which application should be used to open FieldStere project files

Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.

This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.

See the Release Notes: http://avogadro.openmolecules.net/wiki/Avogadro_1.1.0

What does Avogadro do?

• An intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
• Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
• Interfaces to many common computational packages
• Designed to help both educational users and advanced research
• Plugins that allow Avogadro to be extended and customized
• Well defined public API, library and Python bindings for development
• Embedded Python interpreter
• Translations available in 19+ languages

For more information: http://avogadro.openmolecules.net/wiki/

Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-

• View 3D molecular structures, images, and PDFs
• Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
• Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
• Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
• Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
• Distance calculations, structure alignments, anaglyph 3D, and much more

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.

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.

I’ve added CORINA to the alphabetical listing. CORINA is a fast and powerful 3D structure generator for small and medium sized, typically drug-like molecules. Its robustness, comprehensiveness, speed and performance makes CORINA a perfect application to convert large chemical datasets or databases.

YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions.

YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard computers. You can push and pull molecules around and work with dynamic models instead of static pictures.

I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.

iSpartan creates molecules as familiar 2D sketches, directly converts these into 3D structures, and calculates low energy conformations. Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5,000 molecule subset of the Spartan Spectra and Properties Database (SSPD). The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination.

iSpartan Server is an available add-on to the iSpartan app. iSpartan Server installs on a Windows or Macintosh computer and converts iSpartan from an application whose primary utility is sketching molecules in 2D and visualizing them in 3D, into an open-ended molecular modeling research tool providing access to the full Spartan Spectra and Properties Database (SSPD), currently ~170,000 molecules) and to the computational engines used to produce the data in the SSPD. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.

There is a listing of science apps for iOS here

POSIT - Ligand guided pose prediction POSIT is designed to use bound ligand information to improve pose prediction. Using a combination of OpenEye approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose.

NEW FEATURES

The optimizer has been enhanced to produce better aligned structures in certain cases.

BUG FIXES

A memory leak in the optimizer was fixed, POSIT should now properly handle large streams of molecules. The -mcs flag is now turned off by default.  In some cases, the mcs was taking far too long for no real benefit in pose prediction.

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.

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

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.

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.

IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

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.

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.

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)

UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics

This is a major update and whilst some of the new features and tools are described below full details can be found at http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html#1.6. Note this will be the last release supporting Mac PowerPC platforms.

New Tools:

• Animation (Utilities) under development, not fully functional, may change significantly — save/restore Chimera scenes
• Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
• Change Chain IDs (Structure Editing)
• MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
• Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)

• Renumber Residues (Structure Editing)

  New Commands:

• background — set background color(s) or image

• changechains — reassign chain IDs
• fitmap — command implementation of Fit in Map, plus features not available in that tool:
• global search with random initial placement
• sequential fitting of multiple different structures
• symmetric fitting of copies of the same structure
• invert — swap substituents
• resrenumber — renumber residues
• ibclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
• ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and “stiffness” of cardinal spline ribbon
• scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
• zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)

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 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.

I was reading the announcements of new products from OpenEye and I thought I should update the listings.

AFITT from OpenEye is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum. It capitalizes on a combination of core technologies that OpenEye has developed, specifically conformer generation, shape potential, high quality small molecule structure minimization, and visualization. The key step, after finding the appropriate conformers and aligning them to density, is the implementation of a refinement that combines force field and shape potentials, via a series of adiabatic optimizations [1]. The AFITT distribution includes both a GUI and a collection of command-line applications.

BROOD is a software application designed to help project teams in drug discovery explore chemical and property space around their hit or lead molecule. BROOD generates analogs of the lead by replacing selected fragments in the molecule with fragments that have similar shape and electrostatics, yet with selectively modified molecular properties. BROOD fragment searching has multiple applications, including lead-hopping, side-chain enumeration, patent breaking, fragment merging, property manipulation, and patent protection by SAR expansion.

FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.

QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.

SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

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:

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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

CRYSTAL program computes the electronic structure of periodic systems

FITTED has been updated to 2.6.1 and is available for download.