Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
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.
Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
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.
A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
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.
"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.
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.
Science /
Biology /
Biochemistry_and_Molecular_Biology /
Biomolecules /
Proteins_and_Enzymes /
Structure
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