Flexible protein-protein docking.
Predicting the structure of protein-protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutions, and properly dealing with molecular flexibility and conformational changes. Flexibility can be addressed at several levels: implicitly, by smoothing the protein surfaces or allowing some degree of interpenetration (soft docking) or by performing multiple docking runs from various conformations (cross or ensemble docking); or explicitly, by allowing sidechain and/or backbone flexibility. Although significant improvements have been achieved in the modeling of sidechains, methods for the explicit inclusion of backbone flexibility in docking are still being developed. A few novel approaches have emerged involving collective degrees of motion, multicopy representations and multibody docking, which should allow larger conformational changes to be modeled.
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, NL-3584 CH, Utrecht, The Netherlands. a.m.j.j.bonvin@chem.uu.nl
Alexandre M J J
AM
Bonvin
D001665:Binding Sites; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*
D011506:Proteins