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Template-Based Modeling of Protein-RNA Interactions
Zheng, Jinfang Kundrotas, Petras J. Vakser, Ilya A. Liu, Shiyong
Zheng, Jinfang
Kundrotas, Petras J.
Vakser, Ilya A.
Liu, Shiyong
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Abstract
Protein-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.
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2016-09-23
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Public Library of Science
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Template-Based Modeling of Protein-RNA Interactions
Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu
PLoS Comput Biol. 2016 Sep; 12(9): e1005120. Published online 2016 Sep 23. doi: 10.1371/journal.pcbi.1005120