Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.

ABSTRACT: Protein-protein docking procedures typically perform the global scan of the proteins relative positions, followed by the local refinement of the putative matches. Because of the size of the search space, the global scan is usually implemented as rigid-body search, using computationally inexpensive intermolecular energy approximations. An adequate refinement has to take into account structural flexibility. Since the refinement performs conformational search of the interacting proteins, it is extremely computationally challenging, given the enormous amount of the internal degrees of freedom. Different approaches limit the search space by restricting the search to the side chains, rotameric states, coarse-grained structure representation, principal normal modes, and so on. Still, even with th

SUBMITTER: Dauzhenka T 

PROVIDER: S-EPMC6186188 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature