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Bionet.software.x-plor
Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
http://www.bio.net/hypermail/X-PLOR/
GROMOS
A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
http://igc.ethz.ch/gromos/
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/
RAFT
Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
http://zebra.berkeley.edu/raft/
Protein Dynamics, Inc.
Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
http://proteindynamics.com/
Southwest Biotechnology and Informatics Center
Sequence analysis tools including protein classification with the assistance of predicted secondary structure and sequence format tools, available under license from New Mexico State University.
http://www.swbic.org/products/bioinfo/bioinfo.php
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
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.kun.nl/whatif/
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
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
Helical Wheels
Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
http://marqusee9.berkeley.edu/kael/helical.htm
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://www.scripps.edu/brooks/charmm_docs/charmm.html
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.
http://www.scripps.edu/case/Biomer/
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/
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/ghemical/
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/
Folding@home
It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
http://folding.stanford.edu/
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.
http://www.3dgenoscience.com/index.php
Amber
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
http://amber.ch.ic.ac.uk/
YASARA
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
http://www.yasara.org/
DL Poly
A parallel molecular dynamics simulation package.
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
EGO
A parallel program for molecular dynamics simulations of biomolecules.
http://www.lrz-muenchen.de/~heller/ego/
SWISS-MODEL
SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
http://www.expasy.ch/swissmod/SWISS-MODEL.html
GRAMM (Global Range Molecular Matching)
A program for modeling protein docking.
http://reco3.musc.edu/gramm/
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/
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
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/
CADD tools in Drug R&D
PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
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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