Accurate predictions of protein-binding residues (PBRs) enhances understanding of molecular-level rules governing protein-protein interactions, helps protein-protein docking and facilitates annotation of protein functions. Recent studies show that current sequence-based predictors of PBRs severely cross-predict residues that interact with other types of protein partners (e.g. RNA and DNA) as PBRs. Moreover, these methods are relatively slow, prohibiting genome-scale use.