Sampling the conformation of protein surface residues for flexible protein docking

Background: The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins in their unbound state, is a difficult one. The location of the docking interface is determined largely by geometric complementarity, but finding complementary geometry is complicated by the flexibility of the backbone and side-chains of both proteins. We seek to generate candidates for docking that approximate the bound state well, even in cases where there is backbone and/or side-chain difference from unbound to bound states. Results: We divide the surfaces of each protein into local patches and describe the effect of side-chain flexibility on each patch by sampling the space of conformations of its side-chains. Likely positions of individual side-chains are given by a rotamer library; this library is used to derive a sample of possible mutual conformations within the patch. We enforce broad coverage of torsion space. We control the size of the sa...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Patricia Francis-Lyon, Shengyin Gu, Joel Hass, Nina Amenta, Patrice Koehl
• Keywords: BMCBI 2007, BMCBI 2010, Bound State, Protein, Protein Dimers