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» 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
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» Amber
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
http://amber.ch.ic.ac.uk/
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» 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/
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» 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/
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» 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/
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» DL Poly
A parallel molecular dynamics simulation package.
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
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» EGO
A parallel program for molecular dynamics simulations of biomolecules.
http://www.lrz-muenchen.de/~heller/ego/
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» 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
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» Folding@home
It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
http://folding.stanford.edu/
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» 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/
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» 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/
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» Gromacs
A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
http://www.gromacs.org/
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» 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
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» 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
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» 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
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» 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/
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» 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/
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» 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.
http://www.geocities.com/pdbviewer/
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» 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/
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» 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/
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» 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
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» 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
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» Sesame Project
Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
http://www.sesame.wisc.edu/
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» 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/
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» 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/
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» 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/
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» YASARA
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
http://www.yasara.org/
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» 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/
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