Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility

@article{citeulike:2210736, abstract = {A reduced protein model combined with a systematic docking approach has been employed to predict protein-protein complex structures in CAPRI rounds 6-11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to the second protein starting from many thousand initial protein partner placements. It also allows for approximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precalculated soft collective backbone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two targets, and predicted \>20\% correct contacts for five targets. Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed. Proteins 2007. {\copyright} 2007 Wiley-Liss, Inc.}, address = {School of Engineering and Science, Jacobs University Bremen, D-28759 Bremen, Germany}, author = {May, Andreas and Zacharias, Martin }, citeulike-article-id = {2210736}, doi = {http://dx.doi.org/10.1002/prot.21735}, journal = {Proteins: Structure, Function, and Bioinformatics}, keywords = {enm\_application\_docking}, number = {4}, pages = {774--780}, posted-at = {2008-01-09 12:03:06}, priority = {2}, title = {Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility}, url = {http://dx.doi.org/10.1002/prot.21735}, volume = {69}, year = {2007} }

TY - JOUR ID - citeulike:2210736 L3 - citeulike-article-id:2210736 N2 - A reduced protein model combined with a systematic docking approach has been employed to predict protein-protein complex structures in CAPRI rounds 6-11. The docking approach termed ATTRACT is based on energy minimization in translational and rotational degrees of freedom of one protein with respect to the second protein starting from many thousand initial protein partner placements. It also allows for approximate inclusion of global flexibility of protein partners during systematic docking by conformational relaxation of the partner proteins in precalculated soft collective backbone degrees of freedom. We have submitted models for six targets, achieved acceptable docking solutions for two targets, and predicted >20% correct contacts for five targets. Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed. Proteins 2007. © 2007 Wiley-Liss, Inc. IS - 4 JF - Proteins: Structure, Function, and Bioinformatics AD - School of Engineering and Science, Jacobs University Bremen, D-28759 Bremen, Germany EP - 780 TI - Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility VL - 69 SP - 774 KW - enm_application_docking AU - May, Andreas AU - Zacharias, Martin PY - 2007/// UR - http://dx.doi.org/10.1002/prot.21735 ER -