title: Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction.
abstract: A full understanding of the mechanism of post- transcriptional regulation requires more than simple two- state prediction (binding or not binding) for RNA binding proteins. Here we report a sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly accurate complex structure prediction (77% of residues are within 4°A RMSD from native in average for the independent test set) but also achieves the best performing two-state binding or non-binding prediction with an accuracy of 98%, precision of 84%, and Mathews correlation coefficient (MCC) of 0.62. Moreover, it predicts binding residues with an accuracy of 84%, precision of 66% and MCC value of 0.51. In addition, it has a success rate of 77% in predicting RNA binding types (mRNA, tRNA or rRNA). We further demonstrate that it makes more than 10% improvement either in precision or sensitivity than PSI- BLAST, HHPRED and our previously developed structure- based technique. This method expects to be useful for highly accurate genome-scale, high-resolution prediction of RNA-binding proteins and their complex structures. A web server (SPOT) is freely available for academic users at http://sparks.informatics.iupui.edu.
authors.affiliation: School of Informatics, Indiana University Purdue University, Indianapolis, IN, USA.
authors.forename: Huiying
authors.initials: H
authors.lastname: Zhao
authors.forename: Yuedong
authors.initials: Y
authors.lastname: Yang
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D017510:Protein Folding; D012333:RNA, Messenger / Q000378:metabolism; D012335:RNA, Ribosomal / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D016601:RNA-Binding Proteins; D012343:RNA, Transfer