title: A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data.
abstract: We present here an extended protein-RNA docking benchmark composed of 71 test cases in which the coordinates of the interacting protein and RNA molecules are available from experimental structures, plus an additional set of 35 cases in which at least one of the interacting subunits is modeled by homology. All cases in the experimental set have available unbound protein structure, and include five cases with available unbound RNA structure, four cases with a pseudo-unbound RNA structure, and 62 cases with the bound RNA form. The additional set of modeling cases comprises five unbound-model, eight model-unbound, 19 model-bound, and three model-model protein-RNA cases. The benchmark covers all major functional categories and contains cases with different degrees of difficulty for docking, as far as protein and RNA flexibility is concerned. The main objective of this benchmark is to foster the development of protein-RNA docking algorithms and to contribute to the better understanding and prediction of protein-RNA interactions. The benchmark is freely available at http://life.bsc.es/pid/protein-rna-benchmark.
authors.affiliation: Joint BSC-IRB research programme in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Barcelona 08034, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Pérez-Cano
authors.forename: Brian
authors.initials: B
authors.lastname: Jiménez-García
authors.forename: Juan
authors.initials: J
authors.lastname: Fernández-Recio
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA