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dc.contributor.authorZheng, Jinfang
dc.contributor.authorKundrotas, Petras J.
dc.contributor.authorVakser, Ilya A.
dc.contributor.authorLiu, Shiyong
dc.identifier.citationZheng J, Kundrotas PJ, Vakser IA, Liu S (2016) Template-Based Modeling of Protein-RNA Interactions. PLoS Comput Biol 12(9): e1005120.
dc.description.abstractProtein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.en_US
dc.publisherPublic Library of Scienceen_US
dc.rights© 2016 Zheng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.titleTemplate-Based Modeling of Protein-RNA Interactionsen_US
kusw.kuauthorVakser, Ilya A.
kusw.kudepartmentMolecular Biosciencesen_US
kusw.oaversionScholarly/refereed, publisher versionen_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US

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