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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.
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.
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.
ModBase
a searchable database of three-dimensional protein models calculated by comparative modeling based on the programs PSI-BLAST and MODELLER.
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.
The RCSB Protein Data Bank
A free repository of protein structures in a standard file format (pdb).
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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