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. |
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. |
