Protein-Protein Docking with Backbone Flexibility

@article{citeulike:1702029, abstract = {Computational protein-protein docking methods currently can create models with atomic accuracy for protein complexes provided that the conformational changes upon association are restricted to the side chains. However, it remains very challenging to account for backbone conformational changes during docking, and most current methods inherently keep monomer backbones rigid for algorithmic simplicity and computational efficiency. Here we present a reformulation of the Rosetta docking method that incorporates explicit backbone flexibility in protein-protein docking. The new method is based on a "fold-tree" representation of the molecular system, which seamlessly integrates internal torsional degrees of freedom and rigid-body degrees of freedom. Problems with internal flexible regions ranging from one or more loops or hinge regions to all of one or both partners can be readily treated using appropriately constructed fold trees. The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models.}, author = {Wang, Chu and Bradley, Philip and Baker, David }, citeulike-article-id = {1702029}, comment = {Rosetta Dock with flexibility}, doi = {http://dx.doi.org/10.1016/j.jmb.2007.07.050}, journal = {Journal of Molecular Biology}, keywords = {docking, flexibility, modeling, theory}, month = {October}, number = {2}, pages = {503--519}, posted-at = {2008-04-07 14:23:45}, priority = {2}, title = {Protein-Protein Docking with Backbone Flexibility}, url = {http://dx.doi.org/10.1016/j.jmb.2007.07.050}, volume = {373}, year = {2007} }

TY - JOUR ID - citeulike:1702029 L3 - citeulike-article-id:1702029 TI - Protein-Protein Docking with Backbone Flexibility JF - Journal of Molecular Biology VL - 373 IS - 2 SP - 503 EP - 519 N2 - Computational protein-protein docking methods currently can create models with atomic accuracy for protein complexes provided that the conformational changes upon association are restricted to the side chains. However, it remains very challenging to account for backbone conformational changes during docking, and most current methods inherently keep monomer backbones rigid for algorithmic simplicity and computational efficiency. Here we present a reformulation of the Rosetta docking method that incorporates explicit backbone flexibility in protein-protein docking. The new method is based on a "fold-tree" representation of the molecular system, which seamlessly integrates internal torsional degrees of freedom and rigid-body degrees of freedom. Problems with internal flexible regions ranging from one or more loops or hinge regions to all of one or both partners can be readily treated using appropriately constructed fold trees. The explicit treatment of backbone flexibility improves both sampling in the vicinity of the native docked conformation and the energetic discrimination between near-native and incorrect models. KW - docking KW - flexibility KW - modeling KW - theory N1 - Rosetta Dock with flexibility AU - Wang, Chu AU - Bradley, Philip AU - Baker, David PY - 2007/10/19/ UR - http://dx.doi.org/10.1016/j.jmb.2007.07.050 ER -