Sampling the conformation of protein surface residues for flexible protein docking.

ABSTRACT:

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 individ

SUBMITTER: Francis-Lyon P 

PROVIDER: S-EPMC3002368 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature