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.
- http://brooks.scripps.edu/charmm_docs/TSRI_docs-list.htm

Molecular Modeling on Your Home Computer
- Introduction to a quick, simple, and free way to model molecules.
- http://jrgm.ourprofile.org/

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.
- http://www.uku.fi/~thassine/projects/ghemical/

BioAdviser
- Package for displaying, analyzing, and manipulating 3D structures of biological macromolecules, with special emphasis on the study of proteins and enzymes. Includes links to other products by FQS Poland, in Krakow.
- http://www.fqspl.com.pl/bioadviser/

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.
- http://www.3dgenoscience.com/

SWISS-MODEL
- SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
- http://swissmodel.expasy.org//SWISS-MODEL.html

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.
- http://www.zmmsoft.com/

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.
- http://www.psc.edu/~deerfiel/PSdb/

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.
- http://www.cmbi.ru.nl/whatif/

RAMP
- Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
- http://software.compbio.washington.edu/ramp/ramp.html

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.
- http://dasher.wustl.edu/

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.
- http://www.imb-jena.de/IMAGE.html

Sesame Project
- Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
- http://www.sesame.wisc.edu/

Helical Wheels
- Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
- http://kael.net/helical.htm

CADD tools in Drug R&D
- PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
- http://home.pchome.com.tw/team/gentamicin/mol/mol.htm

ChemVis
- Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in Nürnberg, Germany.
- http://www2.chemie.uni-erlangen.de/projects/ChemVis/

Highlights of Biochemistry
- Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
- http://www.biologie.uni-hamburg.de/lehre/bza/eanfang.htm

Pande Group
- Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
- http://www.stanford.edu/group/pandegroup/

EGO
- A parallel program for molecular dynamics simulations of biomolecules.
- http://www.lrz-muenchen.de/~heller/ego/

DL Poly
- A parallel molecular dynamics simulation package.
- http://www.cse.clrc.ac.uk/msi/software/DL_POLY/

YASARA
- (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
- http://www.yasara.org/

Amber
- A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
- http://amber.ch.ic.ac.uk/

Folding@home
- It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
- http://folding.stanford.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.
- http://dasher.wustl.edu/tinker/

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.
- http://www.scripps.edu/pub/olson-web/doc/autodock/

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 ann
- http://www.scripps.edu/case/Biomer/

EGO VIII
- A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
- http://www.lrz-muenchen.de/~heller/ego/egointro.html

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.
- http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

RAFT
- Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
- http://zebra.berkeley.edu/raft/

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.
- http://www.ks.uiuc.edu/Research/namd/

GROMOS
- A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
- http://igc.ethz.ch/gromos/

X-plor Archives
- Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
- http://www.bio.net/hypermail/X-PLOR/