Accounting for large amplitude protein deformation during in silico macromolecular docking.

摘要: Rapid progress of theoretical methods and computer calculation resources has turned in silico into a conceivable tool to predict the 3D structure macromolecular assemblages, starting from their separate elements. Still, some classes complexes represent real challenge for docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling surface accessible partner DNA. We discuss problems linked with managing such rearrangements we review strategies that are presently being explored, as well limitations success.