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AMMP and Related Molecular Modeling Software - Full-featured molecular mechanics, dynamics and modeling program.
Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
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. - 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.
MODELLER Page at The Rockefeller University - A program for homology protein structure modelling by satisfaction of spatial restraints.
ModBase - a searchable database of three-dimensional protein models calculated by comparative modeling based on the programs PSI-BLAST and MODELLER.
NAMD - Scalable Molecular Dynamics - High-performance simulation of large biomolecular systems
TINKER Molecular Modeling Package - Package for molecular mechanics and dynamics, with some special features for polypeptides.
The RCSB Protein Data Bank (PDB) - Archive of experimentally-determined, biological macromolecule 3-D structures from the Brookhaven National Laboratory.
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.
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