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VISUALISATION
ATOMISTIC SIMULATIONS
MESOSCOPIC SIMULATIONS
MOLECULAR MODELLING
FORCE FIELD DEVELOPMENT
QUANTUM CHEMISTRY
QM/MM
FIRST PRINCIPLES SIMULATIONS
MULTI-SCALE
POISSON-BOLTZMANN SOLVERS
DRUG DESIGN
DOCKING
CRYSTALLOGRAPHY
BIOINFORMATICS (incl. tutorials)
CELLULAR AUTOMATA
COMPUTATIONAL CELL BIOLOGY
COMPUTATIONAL MATERIALS SCIENCE
KINETIC MODELLING
LATTICE BOLTZMANN
THERMODYNAMIC AND PROCESS SIMULATION
BIOSTRUCTURE SERVERS & DOWNLOAD PAGES
DATABASES & MISCELLANEOUS TOOLS
LINKS TO OTHER SOFTWARE LISTS
MISCELLANEOUS

VISUALISATION

Freeware from ACD
ArgusLab - molecular modeling, graphics, and drug design program
Ascalaph Quantum - PC interface for GAMESS
ChemCraft - Windows-based graphical program for working with quantum chemistry computations with (Gaussian & Gamess-US)
Chimera (former Midas+) - Interactive visualisation/analysis tool
Chime - from Elsevier MDL
DeepView - Swiss-PdbViewer (tutorial)
Discovery from Accelrys
gOpenMol by Leif Laaksonen
Molden - a pre- and post processing program of molecular and electronic structure
MovieMol - easy-to-use molecular display/animation program
PovRay modeller
Pymol molecular visualization system
RASMOL - Molecular visualization software
VMD - visual molecular dynamics
xmgrace for WYSIWYG 2D plotting

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ATOMISTIC SIMULATIONS

Amber - Assisted Model Building with Energy Refinement
CHARMM - for Macromolecular Energy, Minimization, and Dynamics Calculations
DL_POLY general purpose serial and parallel molecular dynamics simulation package
Gromacs versatile package to perform molecular dynamics
M.DynaMix - a general purpose scalable parallel molecular dynamics
Moldy - a general-purpose molecular dynamics simulation program
NAMD a parallel MD code designed for high-performance simulation
ProtoMol is an object-oriented, component based, framework for MD simulations
Q - MD package designed for free energy calculations in biomolecular systems
VMD - visual molecular dynamics

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MESOSCOPIC SIMULATIONS

DL_MESO mesoscale simulation package
ESPResSo - Extensible Simulation Package for Research on Soft matter
MesoRD is a tool for stochastic simulation of reactions and diffusion

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MOLECULAR MODELLING

ArgusLab - A molecular modeling, graphics, and drug design program
HyperChem - Molecular modelling
MacroModel - versatile, full-feature program for modelling.
Maestro - Graphical interface between Jaguar and MacroModel
Molecular models from Indico Instruments (no computer needed)
TINKER - Software Tools for Molecular Design
WhatIf - molecular modelling

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FORCE FIELD DEVELOPMENT

Empirical Force Field Development Resources from Alex Mackerell
RESP/ESP charge derivation page by François Dupradeau
Automatic force field parameter assignment in YASARA

MM and FF reference list

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QUANTUM CHEMISTRY

ADF - Amsterdam density functionals
CRYSTAL - computes the electronic structure of periodic materials.
DALTON - is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
deMon - density of Montreal A software package for density functional theory (DFT) calculations.
GAMESS-US - General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package.
GAMESS-UK
Gaussian - is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.
Jaguar - rapid ab initio electronic structure package.
MOLCAS - "MOLCAS - A general QC software with emphasis on multiconfigurational methods for large molecules and heavy element chemistry, including also programs for DFT, MP2, CC, etc. calculations".
Molpro is a complete system of ab initio programs for molecular electronic structure calculations
NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters.
ODYSSEY - software for undergraduate students
ORCA - a modern electronic structure program package
PyQuante - is an open-source suite of programs for developing quantum chemistry methods, written in Python.
Q-Chem - ab initio quantum mechanics
Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms)
Spartan - molecular mechanics and quantum chemistry
Turbomole - a powerful quantum chemistry package.

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QM/MM

Chemshell
QMMM 1.3

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FIRST-PRINCIPLES SIMULATIONS

VAMP/VASP - AIMD using pseudopotentials and a plane wave basis set
CPMD - a plane wave/pseudopotential implementation of DFT for AIMD
CP2K - Ist principles MD for solid, liquid and biological systems


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MULTI-SCALE

ChemShell is a computational chemistry environment, based on the Tcl interpreter.
Multiscale-scale & multu fidelity software from CFDRC
OCTA - multiscale modelling

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POISSON-BOLTZMANN SOLVERS

Delphi - linear/nonlinear form for molecules of arbitrary shape/charge distribution

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DRUG DESIGN

ArgusLab software
Drug Design Optimization Lab (D2OL)
Software from RELIC
Otava - drug discovery software
Desert Scientific Software
Drug Discovery Software from Quantum Pharmaceuticals
Molecular Discovery software list
QuantumLead software
RACHEL from Drug Design Methodologies
ScenceServe software
Simulated Biomolecular Systems software
VEGA and other software from Drug Design Laboratory

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DOCKING
AutoDock
Dock 6.1

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CRYSTALLOGRAPHY
HKL Research: Denzo X-ray/synchrotron software
Solve/Resolve - Crystallography software
Uppsala Software Factory - Software and Resources for Macromolecular Crystallography and Structural Biology

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BIOINFORMATICS

Arne Elofsson's bioinformatics software
Andrew C.R. Martin's group in UCL
Barton group in Dundee
Bioinformatics.org
Bioinformatics Software for Mac OS X by Mike Robeson
BiRC software list
Blast
CASP ( protein structure prediction center)
Crystallography and Bioinformatics - University of Cambridge servers
FSA-Blast (faster-search algorithm Blast)
ClustalW2 for multiple sequence analysis
CGB Bioinformatics portal software
CLCBio software
CompBio software
EPSRC National Service for Computational Chemistry Software
Leipzig university list
MCIC's list
Netsci software list
Mobyle of Instute Pasteur (portal)
Modeller comparative modeling
Ohio Supercomputer center's list
PSIPRED (protein structure prediction server)
SWISS-MODEL fully automated protein structure homology-modeling server
Software from SPSoft
Software from Blueprint
Sybyl - Protein modelling
Tubingen University list
WEHI bioinformatics list
WHAT IF a versatile molecular modelling package
WHAT IF server
3D-JigSaw comparative modelling (server)

Other software lists:
EMBL - list of structure prediction software
Homology modelling link list (dkfz)

Tutorials in Bioinformatics:
Homology modelling (by Arne Elofsson)
Homology modelling (by Gert Vriend)
Homology modelling for beginners (by Gert Vriend)
A guide to Structure prediction (by Rob Russell - EMBL)
Protein modelling for grand parents (by Stewart Adcock and Jens Nielsen)
Molecular Modelling (by Bengt Persson)
On-line lectures on Bioinformatics (MPG)
Bioinformatics and homology modelling (by Gale Rhodes)
Bioinformatics: A tutorial for beginners (by Gale Rhodes)
Bioinformatics Genomics (by Donald Forsdyke)
Python course on Bioinformatics (by Katja Schuerer and Catherine Letondal)
Biopython tutorial and cook book (by Hang, Chapman & Friedberg)
Bioinformatics: On-line courses and tutorials
Bioinformatics: Related articles and tutorials
Bioinformatics tools
Bioinformatics tutorials (UBiC)
Bioinformatics tutorials (eBioinfogen)
EMBO Bionformatics tutorial
Bioinformatics, sequence and structural alignment (UIUC)
MyBio.net tutorials links
Bioinformatics.org tutorial
Bioinformatics courses around the world (by Steve Bottomley)
UNC tutorials/course packets for Bioinformatics
Yale Bioinformatics Introduction

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CELLULAR AUTOMATA
CAPOW 2005
Cellab by John Walker and Rudy Rucker (user guide)
Five cellular automata
Mirek's Cellebration
SARCASim
TREND & jTREND
Wolfram MathWorld

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COMPUTATIONAL CELL BIOLOGY
NRCAM - Cell analysis and modelling

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KINETIC MODELLING

MKM - microkinetic modelling
KMC - from materials computation center (UIUC)

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LATTICE BOLTZMANN

OpenLB - open source Lattice-Boltzmann code
- interested in LB ? Join the mailing list

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THERMODYNAMIC AND PROCESS SIMULATION

ProSim - process simulation software

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COMPUTATIONAL MATERIALS SCIENCE

Advanced materials science tools from ACD
GULP General Utility Lattice Program (documentation)
Software from The computational materials science group of CLRC
ESM - software for materials science and thermochemistry
Materials Studio - Collection of modelling software from Accelrys
Materials explorer - a multi-purpose molecular dynamics software package
Software and image analysis software list and links from Materials Today
Materials software + tools list from NPL

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BIOSTRUCTURE SERVERS & DOWNLOAD PAGES

Bioinformatic Tool Server @utomaticTOME
CBS server
The Dundee PRODRG2 sever
Sven Hovmöller's server for Protein Shape Strings and DNA sequences
Morph Server for multiple subunits and nucleic acids
PeptGen - Creates sets of overlapping peptides for proteins to aid in peptide design for mapping epitopes
Topology of Protein Structure (TOPS) server
The PSIPRED Protein Structure Prediction Server
PredictProtein server
ExPASy Proteomics Server
Protein analysis toolkit server (PAT)
WebQC - Molecular Formats Converter

Mikko Karttunen's lipid membrane downloads
Thieleman's lipid membrane downloads
Scott Feller's lipid membrane downloads
Helmut Heller's lipid membrane downloads

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DATABASES & MISCELLANEOUS TOOLS AND TIPS

Software and Databases for Computational Biology - suplementary to the book by Steven Salzberg, David Searls, and Simon Kasif
Pekka Pyykkö's database on relativistic Quantum Chemistry.
Macromolecular structure database - ligand chemistry
Klotho: Biochemical Compounds Declarative Database
JENA library - Atlas of Macromolecule Structures database
The knottin database - standardized data on the knottin structural family
MARTINDALE'S THE REFERENCE DESK: CHEMICAL & BIOCHEMICAL DATABASES
Nucleic Acid Database at Rutgers
OSIRIS Property explorer
PCOD - Predicted Crystallography Open Database & PPDF Predicted Powder Diffraction File (software)
Protein Data Bank
Umber databank
Protein Sequence Data Bank

Baaden IBPC software & scripts
SIMULAID: a collection of utilities
The MDTools suite is a collection of programs, scripts, and utilities
Pim Schravendijk's MD tips from
Oliver Beckstein's software page
DSSP program - to standardize secondary structure assignment
Andrey's DNA/RNA records for OPLS force field in GROMACS forma
Babel - A Molecular Structure Information Interchange Hub - interconversion between different topology file formats
BMEsource - a shared web portal for the biomedical technology
John Kerrigans Structural Bioinformatics page
Gale Rhodes Molecular level
Robert Campbell's modelling and crystallography page

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LINKS TO OTHER SOFTWARE LISTS

ASA - Alabama supercomputer authority software list
Andrew C.R. Martin's software page
BioChemWeb - Ukrainian Bioorganic Chemistry resource
Chemistry resources worldwide - software
Eric Martz' Free Molecular Visualization and Modeling Software
CMM software list
CCP5 - program library
CCL - Computational Chemistry List's software catalog
CompuChem - software list
Computational Chemistry software - compiled by David W Brooks
Linux4Chemistry - extensive list over many categories!
MC2 software list
Materials computation center software archive
Schrodinger - product list
NetSci's list of software for quantum mechanics
Parallel Quantum Chemistry Software at Programs For All
Quantum Chemistry Program Exchange (QPCE) promotes the practice of computational chemistry by gathering and distributing computer software for chemistry and related fields.
Quantum Chemistry software list from McGill Univeristy
Quantum Chemistry software list - compiled bt Txoni
Chemistry software list from Trinity university
Rolf Claessen's Chemistry index.
Software list from Chemistry at FU Berlin (not maintained anymore)
Software list from College of Natural Sciences, Chonnam National University, Korea
Science Software Services from ScienceDownload.com
Techion Taub computer center's software list
Tom's free Chemistry software
WWW.SG-CHEM.NET - software from Dr. S. I. Gorelsky.

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MISCELLANEOUS

Quantum Chemistry software manuals from Charles Darwin Chemistry (AU)
A molecular Dynamics primer

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