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Software
Top > Biology > Biochemistry and Molecular Biology > Biomolecules > Software
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Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
Details Hits: 0 Votes: 0 Ratings: 
Reviews: 
Google PR: 2. 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.
Details Hits: 1 Votes: 0 Ratings: Reviews: Google PR: 3. RAFT
Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 4. 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.
Details Hits: 1 Votes: 0 Ratings: Reviews: Google PR: 5. EGO VIII
A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: (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.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 7. 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.
Details Hits: 3 Votes: 0 Ratings: Reviews: Google PR: 8. TINKER
A free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. Distributed as source code and as binaries for Windows9x, Linux and Mac.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 9. Folding@home
It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
Details Hits: 2 Votes: 0 Ratings: Reviews: Google PR: 10. Amber
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 11. YASARA
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 12. DL Poly
A parallel molecular dynamics simulation package.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 13. EGO
A parallel program for molecular dynamics simulations of biomolecules.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 14. Pande Group
Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 16. ChemVis
Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in NALrnberg, Germany.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 17. D
PSCAN, PMOL2Q, DBFILTER download page. Taichung, Taiwan.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR: 18. PDB Viewer
Downloads for Windows and Linux, to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates, from ex-student at University of Manchester, England.
Details Hits: 1 Votes: 0 Ratings: Reviews: Google PR: 19. Helical Wheels
Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
Details Hits: 4 Votes: 0 Ratings: Reviews: Google PR: 20. Sesame Project
Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
Details Hits: 0 Votes: 0 Ratings: Reviews: Google PR:
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