title: A non-redundant protein-RNA docking benchmark version 2.0.
abstract: We present an updated version of the protein-RNA docking benchmark, which we first published four years back. The non-redundant protein-RNA docking benchmark version 2.0 consists of 126 test cases, a threefold increase in number compared to its previous version. The present version consists of 21 unbound-unbound cases, of which, in 12 cases, the unbound RNAs are taken from another complex. It also consists of 95 unbound-bound cases where only the protein is available in the unbound state. Besides, we introduce 10 new bound-unbound cases where only the RNA is found in the unbound state. Based on the degree of conformational change of the interface residues upon complex formation the benchmark is classified into 72 rigid-body cases, 25 semiflexible cases and 19 full flexible cases. It also covers a wide range of conformational flexibility including small side chain movement to large domain swapping in protein structures as well as flipping and restacking in RNA bases. This benchmark should provide the docking community with more test cases for evaluating rigid-body as well as flexible docking algorithms. Besides, it will also facilitate the development of new algorithms that require large number of training set. The protein-RNA docking benchmark version 2.0 can be freely downloaded from http://www.csb.iitkgp.ernet.in/applications/PRDBv2. Proteins 2017; 85:256-267. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India.
authors.forename: Chandran
authors.identifier: 0000-0001-8212-6093
authors.initials: C
authors.lastname: Nithin
authors.affiliation: Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India.
authors.forename: Sunandan
authors.initials: S
authors.lastname: Mukherjee
authors.affiliation: Computational Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302, India.
authors.forename: Ranjit Prasad
authors.initials: RP
authors.lastname: Bahadur
mesh_terms: D000465:Algorithms; D000818:Animals; D001419:Bacteria / Q000737:chemistry; D019985:Benchmarking; D030562:Databases, Protein; D066264:Datasets as Topic; D006801:Humans; D051379:Mice; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D012984:Software; D013816:Thermodynamics; D003313:Zea mays / Q000737:chemistry
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: conformation change; protein-RNA complex; protein-RNA docking; protein-RNA interaction; protein-RNA interface