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Amber
37187
Amber
http://amber.ch.ic.ac.uk/
A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
Biology > Biochemistry and Molecular Biology > Biomolecules > Software
molecular dynamics proteins nucleicacids biomolecular simulation peter kollman david case
Jan 6, 2008
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Other links at Biology > Biochemistry and Molecular Biology > Biomolecules > Software
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Rapid Autonomous Fragment Test: interface to search library of known protein folds for automously folding units and subdomains.
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2. ChemVis
Visualization of physico-chemical structures in VML, from research at the Universities of Stuttgart and Erlangen in NALrnberg, Germany.
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3. 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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4. EGO
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5. 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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6. 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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7. YASARA
(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
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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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9. 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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10. EGO VIII
A program to perform molecular dynamics simulations on parallel as well as on sequential computers.
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