title: Sequence-Based Prediction of RNA-Binding Residues in Proteins.
abstract: Identifying individual residues in the interfaces of protein-RNA complexes is important for understanding the molecular determinants of protein-RNA recognition and has many potential applications. Recent technical advances have led to several high-throughput experimental methods for identifying partners in protein-RNA complexes, but determining RNA-binding residues in proteins is still expensive and time-consuming. This chapter focuses on available computational methods for identifying which amino acids in an RNA-binding protein participate directly in contacting RNA. Step-by-step protocols for using three different web-based servers to predict RNA-binding residues are described. In addition, currently available web servers and software tools for predicting RNA-binding sites, as well as databases that contain valuable information about known protein-RNA complexes, RNA-binding motifs in proteins, and protein-binding recognition sites in RNA are provided. We emphasize sequence-based methods that can reliably identify interfacial residues without the requirement for structural information regarding either the RNA-binding protein or its RNA partner.
authors: USDA-ARS, Ames, IA, 50011, USA.
authors: Rasna R
authors: RR
authors: Walia
authors: College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA.
authors: Yasser
authors: Y
authors: El-Manzalawy
authors: College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802, USA.
authors: Vasant G
authors: VG
authors: Honavar
authors: Genetics, Development and Cell Biology Department, Iowa State University, 3112 Molecular Biology Building, Ames, IA, 50011-3650, USA. ddobbs@iastate.edu.
authors: Drena
authors: D
authors: Dobbs
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D001665:Binding Sites; D019295:Computational Biology; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D012984:Software
chemical_list: D011506:Proteins; D016601:RNA-Binding Proteins
keywords: Binding site prediction; FastRNABindR; Homology-based prediction; Machine learning; PS-PRIP; Protein–RNA interfaces; RNA-binding proteins (RBPs); RNABindRPlus; Ribonucleoprotein particles (RNPs); SNBRFinder