title: CAPRI targets T29-T42: proving ground for new docking procedures.
abstract: The critical assessment of protein interactions (CAPRI) experiment provides a unique opportunity for unbiased assessment of docking procedures. The recent CAPRI targets T29-T42 entailed docking of bound, unbound, and modeled structures, presenting a wide range of prediction difficulty. We submitted accurate predictions for targets T40, T41, and T42, a good prediction for T32 and acceptable predictions for T29 and T34. The accuracy of our docking results generally matched the prediction difficulty; hence, docking of modeled proteins produced less accurate results. However, there were interesting exceptions: an accurate prediction was submitted for the dimer of modeled tetratricopeptide repeat (T42) and only an acceptable prediction for the bound/unbound case T29. The ensembles of docking models produced in the scans included an acceptable or better prediction for every target. We show here that our recently developed postscan reevaluation procedure, which tests propensity and solvation measures of the whole interface and the interface core, successfully distinguished these predictions from false docking models. For enzyme-inhibitor targets, we show that the distance of the interface from the enzyme's centroid ranked high native like docking models. Also, for one case we demonstrate that docking of an ensemble of conformers produced by normal modes analysis can improve the accuracy of the prediction.
authors.affiliation: Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel. miriam.eisenstein@weizmann.ac.il
authors.forename: Miriam
authors.initials: M
authors.lastname: Eisenstein
authors.forename: Avraham
authors.initials: A
authors.lastname: Ben-Shimon
authors.forename: Ziv
authors.initials: Z
authors.lastname: Frankenstein
authors.forename: Noga
authors.initials: N
authors.lastname: Kowalsman
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins