Modelling

Protocols

General

• Modeller
• Homology Modelling
• Coot and WinCoot for X-ray Crystallography Model Building
• SynBioSS

Protein Engineering

• Rosetta [1]
• Rosie server [2]
• Rosetta design server [3]

Molecular Dynamics

• Model building and input generation [4]
• NAMD [5]
• OpenMM [6]
• Gromacs [7]
• LAMMPS [8]
• AMBER [9]
• CHARMM [10]

Lab-specific protocols

• Wikiomics:Docking toolbox