Campus Units

Genetics, Development and Cell Biology, Genome Informatics Facility, Bioinformatics and Computational Biology

Document Type

Conference Proceeding

Publication Date


Journal or Book Title

Biocomputing 2016: Proceedings of the Pacific Symposium

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Last Page




Conference Title

Pacific Symposium

Conference Date

January 4–8, 2016


Kohala Coast, HI, United States


Efforts to predict interfacial residues in protein-RNA complexes have largely focused on predicting RNA-binding residues in proteins. Computational methods for predicting protein-binding residues in RNA sequences, however, are a problem that has received relatively little attention to date. Although the value of sequence motifs for classifying and annotating protein sequences is well established, sequence motifs have not been widely applied to predicting interfacial residues in macromolecular complexes. Here, we propose a novel sequence motif-based method for “partner-specific” interfacial residue prediction. Given a specific protein-RNA pair, the goal is to simultaneously predict RNA binding residues in the protein sequence and protein-binding residues in the RNA sequence. In 5-fold cross validation experiments, our method, PS-PRIP, achieved 92% Specificity and 61% Sensitivity, with a Matthews correlation coefficient (MCC) of 0.58 in predicting RNA-binding sites in proteins. The method achieved 69% Specificity and 75% Sensitivity, but with a low MCC of 0.13 in predicting protein binding sites in RNAs. Similar performance results were obtained when PS-PRIP was tested on two independent “blind” datasets of experimentally validated protein- RNA interactions, suggesting the method should be widely applicable and valuable for identifying potential interfacial residues in protein-RNA complexes for which structural information is not available. The PS-PRIP webserver and datasets are available at:


This proceeding is from Biocomputing 2016: pp. 445-455, doi:10.1142/9789814749411_0041 . Posted with permission.


Open Access chapter published by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.

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World Scientific



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