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• Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
• AMMP - 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.
• 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.
• B: On-line Molecular Modeling - "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.
• Biomolecular Modeling Information Server - Web resources including: theory and methods of computational modeling, alphabetical software and database directory.
• Bionet.software.x-plor - Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
• CHARMM - A program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images.
• EGO VIII - A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
• Folding@home - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
• Genmol - Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for Disease Management, Drug Discovery and Development of molecules.
• 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.
• GROMOS - A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
• Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
• MODELLER - A program for homology protein structure modeling by satisfaction of spatial restraints. Site offers the manual in HTML and some simple examples. Commercial software.
• 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.
• RAFT - Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
• 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.
• 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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