Biomolecules
Biomolecules Links
- 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.
- ModBase a searchable database of three-dimensional protein models calculated by comparative modeling based on the programs PSI-BLAST and MODELLER.
- EGO VIII A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
- Amber A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
- MODELLER Page at The Rockefeller University A program for homology protein structure modelling by satisfaction of spatial restraints.
- GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
- Bionet.software.x-plor Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination.
- 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.
- TINKER Molecular Modeling Package Package for molecular mechanics and dynamics, with some special features for polypeptides.
- 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.
- 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.
- AMMP and Related Molecular Modeling Software Full-featured molecular mechanics, dynamics and modeling program.
- Biomolecular Modeling Information Server Web resources including: theory and methods of computational modeling, alphabetical software and database directory.
- The RCSB Protein Data Bank A free repository of protein structures in a standard file format (pdb).
| Help build the largest human-edited directory on the web. |
| Submit a Site - Open Directory Project - Become an Editor |