This notebook contains material from PyRosetta; content is available on Github.

Docking

Protein–protein docking is the prediction of a complex structure starting from its monomer components. The search space can be extremely large, so large amounts of computational resources are typically required. In this workshop, we will explore several of the techniques briefly; keep in mind that for real applications, many more decoys will need to be tested.

Suggested Readings

  • J. J. Gray et al., “Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations,” J. Mol. Biol. 331, 281-299 (2003).
  • S. Chaudhury & J. J. Gray, “Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles,” J. Mol. Biol. 381, 1068-1087 (2008).

Appendix D:

Running PyRosetta on a Cluster includes more helpful information about using the PyJobDistributor to distribute jobs over multiple computers.

In [ ]:
 

Chapter contributors:

  • Kathy Le (Johns Hopkins University); this chapter was adapted from the PyRosetta book (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte).