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AmberA general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes.
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Folding@homeIt is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases.
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Protein Dynamics, Inc.Molecular dynamics simulation programs for proteins, DNA, and RNA, including 3D viewing of molecules. Offers downloadable demonstration version, from Milpitas California.
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YASARA(Yet Another Scientific Artificial Reality Application) is an interactive real-time molecular dynamics program.
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