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).

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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)

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

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

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

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

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..

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.

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.

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

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/)

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.

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

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/

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)

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.

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.

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.

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