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Home >> Science >> Biology >> Biochemistry and Molecular Biology >> Biomolecules >> Software |
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Bionet.software.x-plor Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination. GROMOS A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. 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. 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. EGO VIII A program to perform molecular dynamics simulations on parallel as well as on sequential computers. 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. 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. AutoDock 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. Ghemical An easy-to-use molecular editor and modeling package with all-atoms molecular mechanics, reduced protein models and links to many common chemistry programs. Ghemical is released under the GNU GPL and includes source code. |
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