See also:

• Science: Biology: Biochemistry and Molecular Biology: Biomolecules: Proteins and Enzymes: Structure  (40)
• Science: Biology: Biochemistry and Molecular Biology: Software  (14)
• Science: Biology: Bioinformatics: Online Services  (152)
• Science: Chemistry: Software  (228)
• Science: Physics: Crystallography: Software  (61)

• 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.
• ChemVis - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
• DL Poly - A parallel molecular dynamics simulation package.
• EGO - A parallel program for molecular dynamics simulations of biomolecules.
• 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.
• Genoscience - 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.
• 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.
• Gromacs - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
• Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
• Highlights of Biochemistry - Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
• IMB Jena Image Library of Biological Macromolecules - 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.
• Jay Ponder Lab - 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.
• Molecular Modeling on Your Home Computer - Introduction to a quick, simple, and free way to model molecules.
• 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.
• Pande Group - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
• PDB Viewer - 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.
• Protein Structure Database - 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.
• RAMP - Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
• Sesame Project - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
• SWISS-MODEL - SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
• 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.
• X-plor Archives - Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
• YASARA - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
• ZMM Software Inc. - 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.