title: Prediction of Disordered RNA, DNA, and Protein Binding Regions Using DisoRDPbind.
abstract: Intrinsically disordered proteins and regions (IDPs and IDRs) are involved in a wide range of cellular functions and they often facilitate interactions with RNAs, DNAs, and proteins. Although many computational methods can predict IDPs and IDRs in protein sequences, only a few methods predict their functions and these functions primarily concern protein binding. We describe how to use the first computational method DisoRDPbind for high-throughput prediction of multiple functions of disordered regions. Our method predicts the RNA-, DNA-, and protein-binding residues located in IDRs in the input protein sequences. DisoRDPbind provides accurate predictions and is sufficiently fast to make predictions for full genomes. Our method is implemented as a user-friendly webserver that is freely available at http://biomine.ece.ualberta.ca/DisoRDPbind/ . We overview our predictor, discuss how to run the webserver, and show how to interpret the corresponding results. We also demonstrate the utility of our method based on two case studies, human BRCA1 protein that binds various proteins and DNA, and yeast 60S ribosomal protein L4 that interacts with proteins and RNA.
authors: Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China.
authors: Zhenling
authors: Z
authors: Peng
authors: Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada, T6G 2V4.|Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Richmond, VA, 23284-3019, USA.
authors: Chen
authors: C
authors: Wang
authors: Department of Molecular Medicineand USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine,University of South Florida, Tampa, FL, 33612, USA.|Institute for Biological Instrumentation, Russian Academy of Sciences, Moscow Region, Pushchino, 142290, Russian Federation.|Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation.
authors: Vladimir N
authors: VN
authors: Uversky
authors: Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Richmond, VA, 23284-3019, USA. lkurgan@vcu.edu.
authors: Lukasz
authors: L
authors: Kurgan
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D064267:Intrinsically Disordered Proteins / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D012984:Software
chemical_list: D064267:Intrinsically Disordered Proteins; D012313:RNA; D004247:DNA
keywords: DisoRDPbind; Intrinsic disorder; Prediction; Protein–DNA interactions; Protein–RNA interactions; Protein–protein interactions