PDbRNAbs: A prediction database of RNA binding sites in amino acid sequence using SVM

摘要

PDbRNAbs (Prediction Database of RNA binding sites) is a computational database that integrates a wealth of information relevant to human protein-RNA binding. The data source (a nonredundant data set of approximately 20000 proteins pertaining to human) was extracted from PDB (Protein Data Bank), and the SVM model was constructed using data instances encoded with three sequence features, including the side chain pKa value, hydrophobicity index and molecular mass of an amino acid [2]. When compared with previous studies, the SVM model appears to be more accurate, and RNA-binding residues can be predicted at 66.28% sensitivity and 69.84% specificity. PDbRNAbs presents an interactive interface for users to query information regarding RNA binding sites prediction in human protein, and also allows users to obtain amino acid sequence annotated with header, acession date, compound, author list,resolution,experiment type (if not X-ray) and crystal unit cell parameters from the CRYST1 record.