BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

Ruben Sanchez-Garcia, C O S Sorzano, J M Carazo, Joan Segura, Alfonso Valencia
2018 Bioinformatics  
Motivation: Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction. Computational approaches are orders of magnitude cheaper and faster than experimental ones, leading to proliferation of multiple methods aimed to predict which residues belong to the interface of an interaction. Results: We present BIPSPI, a new
more » ... hine learning-based method for the prediction of partnerspecific PPI sites. Contrary to most binding site prediction methods, the proposed approach takes into account a pair of interacting proteins rather than a single one in order to predict partnerspecific binding sites. BIPSPI has been trained employing sequence-based and structural features from both protein partners of each complex compiled in the Protein-Protein Docking Benchmark version 5.0 and in an additional set independently compiled. Also, a version trained only on sequences has been developed. The performance of our approach has been assessed by a leaveone-out cross-validation over different benchmarks, outperforming state-of-the-art methods. Availability and implementation: BIPSPI web server is freely available at
doi:10.1093/bioinformatics/bty647 pmid:30020406 fatcat:fmnxxuemvza37kmus4lm5gevsu