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See also:
  • Abalone - Program for bio-molecular modeling, particularly for molecular graphics and dynamics with implicit and explicit water models.
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  • Amber - A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
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  • 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.
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  • Ascalaph Designer - Program for creating molecular models, molecular mechanics simulations and development of the force fields by quantum chemical methods.
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  • 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.
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  • 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.
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  • ChemVis - Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in N├╝rnberg, Germany.
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  • DL Poly - A parallel molecular dynamics simulation package. Offered free of charge under an academic licence to scientists pursuing research of a non-commercial nature.
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  • EGO - A parallel program for molecular dynamics simulations of biomolecules.
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  • Folding@home - It is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
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  • GrAfSS: Graph Theoretic Applications for Structure Searching - Graph theoretic methods for the analysis of structural relationships in biological macromolecules.
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  • Gromacs - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids. It is a free software.
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  • GROMOS - A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
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  • Highlights of Biochemistry - Molecular structures are made visible, dependent on Chime scripts at the Faculty of Biology, University of Hamburg, Germany.
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  • IMB Jena Image Library of Biological Macromolecules - Resource for visualization and analysis of 3D-biopolymer structures; proteins, nucleic acids, carbohydrates, and small molecule ligands. Combines experimental and computer generated models, maintained in Germany.
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  • The Jalview Internal PDB Viewer - Used to visualize three dimensional structure of macromolecules, using protein data bank format for atom coordinates.
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  • Jay Ponder Lab - Graphical user interface to suites of molecular modeling tools, providing an integrated environment for engineering applications. Contacts for the group at Washington University School of Medicine in Saint Louis, Missouri.
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  • 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.
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  • Pande Group - Folding simulations for fusion peptides, proteins and RNA with aim of predicting structure from genome by research at Stanford University, California.
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  • Prion Helical Wheels - Java applet to illustrate alpha-helices, using a traditional helical wheel. Output as Postscript, JPEG, GIF or PICT.
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  • RAMP - Public domain suite of programs to aid in the modeling of protein three-dimensional structures. Tested on Linux and Unix.
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  • Sesame Project - Protein structure-function software in multiple modules, maintained at the University of Wisconsin, Madison.
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  • SWISS-MODEL - SWISS-MODEL is an Automated Protein Modelling Server running at the GlaxoWellcome Experimental Research in Geneva, Switzerland.
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  • 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.
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  • 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. Commercial software.
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  • X-plor Archives - Forum for 3D macromolecular structure determination. Includes links to other Biosci/Bionet newsgroups, maintained at Indiana University, Bloomington.
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  • YASARA - (Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
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  • ZMM Software Inc. - Modeling tool for theoretical studies, employing molecular mechanics approach in combination with Monte Carlo energy minimization algorithm. Downloads on secure server, and contacts in Flamborough, Ontario.
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Last update: January 19, 2014 at 8:54:11 UTC - edit