title: RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.
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.
authors.affiliation: Department of Radiology, Wake Forest University Health Science, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
authors.forename: V
authors.initials: V
authors.lastname: Suresh
authors.affiliation: Department of Radiology, Wake Forest University Health Science, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Liu
authors.affiliation: Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26505, USA.
authors.forename: Donald
authors.initials: D
authors.lastname: Adjeroh
authors.affiliation: Department of Radiology, Wake Forest University Health Science, Medical Center Boulevard, Winston-Salem, NC 27157, USA xizhou@wakehealth.edu.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Zhou
mesh_terms: D000818:Animals; D009690:Nucleic Acid Conformation; D060066:Protein Interaction Maps; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D060388:Support Vector Machine
chemical_list: D022661:RNA, Untranslated; D016601:RNA-Binding Proteins