Document Type
Article
Publication Date
2015
College/Unit
Statler College of Engineering and Mining Resources
Department/Program/Center
Lane Department of Computer Science and Electrical Engineering
Abstract
RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation. The experimental methods to solve RNA-protein interaction prediction problem remain expensive and time-consuming. Here, we present the RPI-Pred (RNA-protein interaction predictor), a new support-vector machine-based method, to predict protein-RNA interaction pairs, based on both the sequences and structures. The results show that RPI-Pred can correctly predict RNA-protein interaction pairs with ∼94% prediction accuracy when using sequence and experimentally determined protein and RNA structures, and with ∼83% when using sequences and predicted protein and RNA structures. Further, our proposed method RPI-Pred was superior to other existing ones by predicting more experimentally validated ncRNA-protein interaction pairs from different organisms. Motivated by the improved performance of RPI-Pred, we further applied our method for reliable construction of ncRNA-protein interaction networks. The RPI-Pred is publicly available at: http://ctsb.is.wfubmc.edu/projects/rpi-pred.
Digital Commons Citation
Suresh, V; Liu, Liang; Adjeroh, Donald; and Zhou, Xiaobo, "RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information" (2015). Faculty & Staff Scholarship. 2251.
https://researchrepository.wvu.edu/faculty_publications/2251
Source Citation
Suresh, V., Liu, L., Adjeroh, D., & Zhou, X. (2015). RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information. Nucleic Acids Research, 43(3), 1370–1379. https://doi.org/10.1093/nar/gkv020
Comments
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.