DRPBind: prediction of DNA, RNA and protein binding residues in intrinsically disordered protein sequences

Abstract

DRPbind predicts three components: deoxyribonucleic acid (DNA) binding, ribonucleic acid (RNA) binding and protein-binding residues of query protein sequences. DRPbind utilizes independent sources of information encoded for each component predictor and relies on the information-rich profiles of protein evolutionary-based features, protein physicochemical-based features, and protein structural-based features. DRPbind employs protein profile-based features extracted from the bigrams of PSSM and HMM profiles. It also extracts features from physicochemical and structural attributes. DRPbind takes primary protein sequences as input, and through the Support Vector Machine (SVM) classifier, it provides the binding prediction. DRPbind is optimized based on a specific binding type and shown superior performance in terms of simultaneously predicting the DNA-binding, RNA-binding and protein-binding residues. The source code is available at https://github.com/roneshsharma/DNA-RNA-Protein-Binding/wiki