Links

AMBER a set of molecular mechanics forcefields and a package of molecular
simulation programs

CHARMM macromolecular dynamics and mechanics package

GROMACS MD package which is fast at calculating non-bonded interactions

GROMOS general purpose MD code for biomolecular systems

NAMD parallel MD code for high-performance simulation of large biomolecular systems

EGO parallel program for MD simulations of biomolecules

DL_POLY a general purpose serial and parallel molecular dynamics simulation package

Desmond parallel MD code for high-performamce simulations of biological systems (commercial version available from Schrodinger)

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GAUSSIAN QM software for the prediction of electronic structure and related properties

GAMESS-US a general ab initio quantum chemistry package

GAMESS-UK based on the original version, developed further at Daresbury Laboratory

MOPAC general purpose semi-empirical quantum mechanics package

ChemShell computational chemistry environment supporting standard quantum chemical and force field calculations, with its main strength in QM/MM hybrid calculations

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scap program for protein side-chain prediction and residue mutation

SCWRL program for prediction of protein side-chain conformations

MODELLER used for homology or comparative modelling of protein three-dimensional structures

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VMD a molecular visualisation program for displaying, animating and analysing large biomolecular systems using 3-D graphics

GRASP molecular visualisation and analysis program, particularly good for displaying surfaces and electrostatic properties

RasMol (and its derivative Protein Explorer) software for looking at macromolecular structure and its relation to function

MolMol molecular graphics program for displaying, analysing and manipulating 3-D structures of biological macromolecules

PyMOL molecular visualisation system

Chimera highly extensible, interactive molecular graphics program (successor to UCSF Midas and MidasPlus)

POV-Ray high quality tool for creating stunning 3-D graphics

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Discovery Studio easy-to-use, graphical interface for powerful drug design and protein modeling research

SYBYL computational informatics software for molecular modellers

MOE fully integrated suite of computational chemistry, molecular modelling and informatics software

PROCHECK checks the stereo chemical quality of a protein structure

Molden software for displaying molecular density from ab initio and semi-empirical packages

SPDBV Swiss-PDBViewer provides a user friendly interface allowing analysis of several proteins at the same time

Babel program for interconversion between many file formats used in molecular modelling and computational chemistry

Curves+ calculates a number of structural parameters for nucleic acids with up to 4 strands

GRID computational procedure for determining energetically favourable binging sites on molecules of known structure

APBS a software package for the evaluation of electrostatic properties

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DOCK docking program for protein-ligand, protein-protein, protein-DNA and DNA-ligand interactions

AutoDock automated docking of flexible ligands to macromolecules

GOLD calculates the docking modes of small molecules into protein binding sites

3D Dock suite of automated docking tools (FTDock, RPScore, MultiDock)

HADDOCK protein-protein docking based on biochemical and/or biophysical information, (web server)

eHiTS fast, flexible docking of whole or partial structures to target receptors

LIGPLOT automatically generates schematic diagrams of protein-ligand interactions for a given PDB file

FlexX ultra-fast and flexible protein-ligand docking for inhibitor enrichment during virtual screening

DrugFinder a free web-based virtual screening service from InhibOx

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Accelrys

TRIPOS

DAYLIGHT Chemical Information Systems, Inc

Chemical Computing Group

Schrodinger

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BBSRC

EPSRC

MRC

Wellcome Trust

Royal Society

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Molecular Graphics and Modelling Society (MGMS)

RSC Molecular Modelling Group (MMG)

Computational Chemistry List (CCL)

British Biophysical Society (BBS)

National Service for Computational Chemistry Software (NSCCS) provide software, specialist consultation, computing resources and software training to support UK academics working across all fields of chemistry

National Biomedical Computational Resource (NBCR) US based network which aims to conduct, catalyse and enable biomedical research by harnessing, developing and deploying forefront computational information and grid technologies

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