title: ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.
abstract: The understanding of folding and function of RNA molecules depends on the identification and classification of interactions between ribonucleotide residues. We developed a new method named ClaRNA for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base-phosphate and base-ribose interactions. The accuracy of ClaRNA is 0.997 for canonical base pairs, 0.983 for non-canonical pairs and 0.961 for stacking interactions. The generalized squared correlation coefficient (GC2) for ClaRNA is 0.969 for canonical base pairs, 0.638 for non-canonical pairs and 0.824 for stacking interactions. The classifier can be easily extended to include new types of spatial relationships between pairs or larger assemblies of nucleotide residues. ClaRNA is freely available via a web server that includes an extensive set of tools for processing and visualizing structural information about RNA molecules.
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland iamb@genesilico.pl.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Waleń
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Chojnowski
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland.
authors.forename: Przemysław
authors.initials: P
authors.lastname: Gierski
authors.affiliation: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland iamb@genesilico.pl.
authors.forename: Janusz M
authors.identifier: http://orcid.org/0000-0002-6633-165X
authors.initials: JM
authors.lastname: Bujnicki
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods; D020407:Internet; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA