title: pyDock scoring for the new modeling challenges in docking: Protein-peptide, homo-multimers, and domain-domain interactions.
abstract: The sixth CAPRI edition included new modeling challenges, such as the prediction of protein-peptide complexes, and the modeling of homo-oligomers and domain-domain interactions as part of the first joint CASP-CAPRI experiment. Other non-standard targets included the prediction of interfacial water positions and the modeling of the interactions between proteins and nucleic acids. We have participated in all proposed targets of this CAPRI edition both as predictors and as scorers, with new protocols to efficiently use our docking and scoring scheme pyDock in a large variety of scenarios. In addition, we have participated for the first time in the servers section, with our recently developed webserver, pyDockWeb. Excluding the CASP-CAPRI cases, we submitted acceptable models (or better) for 7 out of the 18 evaluated targets as predictors, 4 out of the 11 targets as scorers, and 6 out of the 18 targets as servers. The overall success rates were below those in past CAPRI editions. This shows the challenging nature of this last edition, with many difficult targets for which no participant submitted a single acceptable model. Interestingly, we submitted acceptable models for 83% of the evaluated protein-peptide targets. As for the 25 cases of the CASP-CAPRI experiment, in which we used a larger variety of modeling techniques (template-based, symmetry restraints, literature information, etc.), we submitted acceptable models for 56% of the targets. In summary, this CAPRI edition showed that pyDock scheme can be efficiently adapted to the increasing variety of problems that the protein interactions field is currently facing. Proteins 2017; 85:487-496. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Chiara
authors.initials: C
authors.lastname: Pallara
authors.affiliation: Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Brian
authors.initials: B
authors.lastname: Jiménez-García
authors.affiliation: Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Romero
authors.affiliation: Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
authors.forename: Iain H
authors.initials: IH
authors.lastname: Moal
authors.affiliation: Life Sciences Department, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.
authors.forename: Juan
authors.identifier: 0000-0002-3986-7686
authors.initials: J
authors.lastname: Fernández-Recio
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D062105:Molecular Docking Simulation / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry*; D012107:Research Design; D012984:Software; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; D011506:Proteins; D014867:Water
keywords: CAPRI; complex structure; protein-peptide interactions; protein-protein docking; pyDock