Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials

Laura Pérez-Cano, Albert Solernou, Carles Pons, Juan Fernández-Recio

Research output: Chapter in Book/Report/Conference proceedingConference contribution

35 Scopus citations

Abstract

Despite the importance of protein-RNA interactions in the cellular context, the number of available protein-RNA complex structures is still much lower than those of other biomolecules. As a consequence, few computational studies have been addressed towards protein-RNA complexes, and to our knowledge, no systematic benchmarking of protein-RNA docking has been reported. In this study we have extracted new pairwise residue-ribonucleotide interface propensities for protein-RNA, which can be used as statistical potentials for scoring of protein-RNA docking poses. We show here a new protein-RNA docking approach based on FTDock generation of rigid-body docking poses, which are later scored by these statistical residue-ribonucleotide potentials. The method has been successfully benchmarked in a set of 12 protein-RNA cases. The results show that FTDock is able to generate near-native solutions in more than half of the cases, and that it can rank near-native solutions significantly above random. In practically all these cases, our propensity-based scoring helps to improve the docking results, finding a near-native solution within rank 100 in 43% of them. In a remarkable case, the near-native solution was ranked 1 after the propensity-based scoring. Other previously described propensity potentials can also be used for scoring, with slightly worse performance. This new protein-RNA docking protocol permits a fast scoring of rigid-body docking poses in order to select a small number of docking orientations, which can be later evaluated with more sophisticated energy-based scoring functions.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing 2010, PSB 2010
Pages293-301
Number of pages9
StatePublished - Dec 1 2010
Event15th Pacific Symposium on Biocomputing, PSB 2010 - Kamuela, HI, United States
Duration: Jan 4 2010Jan 8 2010

Publication series

NamePacific Symposium on Biocomputing 2010, PSB 2010

Other

Other15th Pacific Symposium on Biocomputing, PSB 2010
Country/TerritoryUnited States
CityKamuela, HI
Period1/4/101/8/10

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