title: Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities.
abstract: Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic experimental structure solving, despite essential to the understanding of these functions, is often difficult and expensive. Docking approaches that have been developed for proteins are often challenging to adapt for RNA because of its inherent flexibility and the structural data available being relatively scarce. In this study we adapted the RosettaDock protocol for protein-RNA complexes both at the nucleotide and atomic levels. Using a genetic algorithm-based strategy, and a non-redundant protein-RNA dataset, we derived a RosettaDock scoring scheme able not only to discriminate but also score efficiently docking decoys. The approach proved to be both efficient and robust for generating and identifying suitable structures when applied to two protein-RNA docking benchmarks in both bound and unbound settings. It also compares well to existing strategies. This is the first approach that currently offers a multi-level optimized scoring approach integrated in a full docking suite, leading the way to adaptive fully flexible strategies.
authors.affiliation: AMIB Project, Inria Saclay-Île de France, Palaiseau, France; Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France; Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Guilhot-Gaudeffroy
authors.affiliation: AMIB Project, Inria Saclay-Île de France, Palaiseau, France; Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Froidevaux
authors.affiliation: AMIB Project, Inria Saclay-Île de France, Palaiseau, France; Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France; Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), CNRS UMR 5506, Université Montpellier 2, Montpellier, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Azé
authors.affiliation: AMIB Project, Inria Saclay-Île de France, Palaiseau, France; Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Bernauer
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012372:ROC Curve; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA