title: RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.
abstract: RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/.
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 Rue Descartes 67000 Strasbourg, France z.miao@ibmc-cnrs.unistra.fr.
authors.forename: Zhichao
authors.identifier: 0000-0002-5777-9815
authors.initials: Z
authors.lastname: Miao
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 Rue Descartes 67000 Strasbourg, France e.westhof@ibmc-cnrs.unistra.fr.
authors.forename: Eric
authors.identifier: 0000-0002-6172-5422
authors.initials: E
authors.lastname: Westhof
mesh_terms: D019985:Benchmarking; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D016208:Databases, Factual; D066264:Datasets as Topic; D020407:Internet; D011336:Probability; D011506:Proteins / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA