Molecular Simulation

This is collection of software and web tools that use to simulate the structure, dynamics and thermodynamics of proteins and other biomolecules. We didn't include in this list many excellent "high-end" multipurpose commercial packages (e.g. Discovery Studio, MOE) which complement the collection here.

Basic concepts: open in new windowIntroduction to Macromolecular Simulation by Peter J. Steinbach

Molecular Mechanics Simulation

Software Use Cost
  Minimizations Molecular Dynamics Monte Carlo QM/MM
3-D visualization
   
AMBER
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Commercial
open in new windowBALLView
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 Free for academics
open in new windowCHARMM
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interface
Commercial
open in new windowGROMACS
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interface
    Free
open in new windowGROMOS96
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       Commercial
open in new windowNAMD
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       Free for academics
open in new windowProtoMol  
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       Free
open in new windowTINKER
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interface
Free
open in new windowVEGA ZZ
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 Free for academics
open in new windowYASARA
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 Commercial
     

Normal Mode Analysis Web Tools

Normal mode analysis (NMA) provides an alternative to molecular dynamics for the study of large-scale collective motions on long timescales of proteins and proteins complexes. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies describe the largest movements in a protein and are the ones that are functionally relevant. The following servers enable calculation of the low frequency normal modes of a proteins and provide various analysis tools.
  Additional Tools:
open in new windowAD-ENM Pathway generation between two conformations, model generation for a protein at an unknown state by using distance constraints for the unknown state (measured by NMR, FRET, etc)
open in new windowelNémo Flexibility analysis by comparison to experimental B-factors, overlap coefficient for two conformations, template generation for molecular replacement
open in new windowNOMAD-Ref Overlap coefficient for two conformations, decoy generation, EM, X-ray and docking refinement, template generation for molecular replacement
open in new windowMolmov NMA Flexibility analysis by comparison to either experimental B-factors or multiple structural alignment
open in new windowoGNM Flexibility analysis by comparison to experimental B-factors, cross-correlation between residue fluctuations
open in new windowWEBnm Pathway generation between two conformations