title: Computational Prediction of RNA-Binding Proteins and Binding Sites.
abstract: Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. jingnasi@bjfu.edu.cn.
authors.forename: Jingna
authors.initials: J
authors.lastname: Si
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. cuijing19900925@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Cui
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. cuijing19900925@163.com.
authors.forename: Jin
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. rwu@bjfu.edu.cn.
authors.forename: Rongling
authors.initials: R
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D064878:Web Browser
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA
keywords: RNA-binding proteins (RBPs); RNA-binding site; bioinformatics; macromolecular docking; prediction