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Folding@home - http://folding.stanford.edu/
It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. |
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Gromacs - http://www.gromacs.org/
A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software. |
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Pande Group - http://www.stanford.edu/group/pandegroup/
Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California. |
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NAMD - http://www.ks.uiuc.edu/Research/namd/
A parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. |
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AutoDock - http://www.scripps.edu/pub/olson-web/doc/autodock/
A suite of automated docking tools. It is designed to predict how small flexible molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. |
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IMB Jena Image Library of Biological Macromolecules - http://www.imb-jena.de/IMAGE.html
Resource for visualization and analysis of 3D-biopolymer structures; proteins, nucleic acids, carbohydrates, and small molecule ligands. Combines experimental and computer generated models, maintained in Germany. |
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Ghemical - http://www.uku.fi/~thassine/projects/ghemical/
An easy-to-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code. |
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DL Poly - http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
A parallel molecular dynamics simulation package. |
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TINKER - http://dasher.wustl.edu/tinker/
A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9x, Linux and Mac. |
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YASARA - http://www.yasara.org/
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program. |
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Sesame Project - http://www.sesame.wisc.edu/
Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison. |
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RAMP - http://software.compbio.washington.edu/ramp/ramp.html
Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix. |
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X-plor Archives - http://www.bio.net/hypermail/X-PLOR/
Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington. |
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Highlights of Biochemistry - http://www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm
Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany. |
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WhatIf - http://www.cmbi.ru.nl/whatif/
Protein structure analysis software for Linux, SGI/IRIX, Windows NT. Performs mutant prediction, structure verification, homology modeling and molecular visualization. Links to the documentation in HTML. Commercial software. |
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Jay Ponder Lab - http://dasher.wustl.edu/
Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washington University School of Medicine in Saint Louis, Missouri. |
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EGO - http://www.lrz-muenchen.de/~heller/ego/
A parallel program for molecular dynamics simulations of biomolecules. |
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B: On-line Molecular Modeling - http://www.scripps.edu/case/Biomer/
"B" (formerly known as Biomer) is a Java-based molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images. |
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ChemVis - http://www2.chemie.uni-erlangen.de/projects/ChemVis/
Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany. |
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AMMP - http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html
A free program suite for molecular mechanics, dynamics and modeling with some special features like docking or ab initio DFT calculations. Runs under Linux/Unix and Win9x. The site provides access to the documentation and offers on-line tutorials. |
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Protein Structure Database - http://www.psc.edu/~deerfiel/PSdb/
PSdb uses primary data, to relate secondary and tertiary information, for solvent accessibility, internal relative distances, and ligand interactions. Maintained at the Mellon Institute, Pittsburgh, Pennsylvania. |
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ZMM Software Inc. - http://www.zmmsoft.com/
Modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure server, and contacts in Flamborough, Ontario. |
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EGO VIII - http://www.lrz-muenchen.de/~heller/ego/egointro.html
A program to perform molecular dynamics simulations on parallel as well as on sequential computers. |
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Genoscience - http://www.3dgenoscience.com/
Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for disease management and drug discovery. Details of company in Marseille, France. |
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Helical Wheels - http://kael.net/helical.htm
Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT. |
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PDB Viewer - http://www.geocities.com/pdbviewer/
Downloads for Windows and Linux, to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates, from ex-student at University of Manchester, England. |
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Molecular Modeling on Your Home Computer - http://jrgm.ourprofile.org/
Introduction to a quick, simple, and free way to model molecules. |
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Amber - http://amber.ch.ic.ac.uk/
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes. |
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SWISS-MODEL - http://swissmodel.expasy.org//SWISS-MODEL.html
SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland. |