Toolbox > Protein Structure > Prediction> Molecular Simulation

Macromolecular Simulations

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: Introduction to Macromolecular Simulation by Peter J. Steinbach

Molecular Mechanics Simulation
Software Use   Cost
 
Minimizations
Molecular Dynamics
Monte Carlo

QM/MM

3-D visualization
   
AMBER
+
+
 
+
  Commercial
BALLView
+
+
 
+
  Free for academics
CHARMM
+
+
+
interface
  Commercial
GROMACS
+
+
 
interface
    Free
GROMOS96
+
+
        Commercial
NAMD
+
+
        Free for academics
ProtoMol  
+
        Free
TINKER
+
+
+
interface
  Free
VEGA ZZ
+
 
+
  Free for academics
YASARA
+
+
 
+
+
  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:
AD-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)
DFprot Protein structure deformability/flexibility analysis
elNémo Flexibility analysis by comparison to experimental B-factors, overlap coefficient for two conformations, template generation for molecular replacement
NOMAD-Ref Overlap coefficient for two conformations, decoy generation, EM, X-ray and docking refinement, template generation for molecular replacement
Molmov NMA Flexibility analysis by comparison to either experimental B-factors or multiple structural alignment
oGNM Flexibility analysis by comparison to experimental B-factors, cross-correlation between residue fluctuations
ProMode Database of normal mode analysis of proteins
UMMS Pathway generation between two conformations, FRET data analysis
WEBnm Pathway generation between two conformations