A novel Greedy approach for Sequence based Computational prediction of Binding-Sites in Protein-Protein Interaction

Abstract

Computational prediction of protein-protein interaction (PPI) from protein sequence is important as many cellular functions are made possible through PPI. The Protein Interaction Prediction Engine (PIPE) software suite was developed for such predictions. The specific location of interaction is predicted by the PIPE-Sites predictor, which depends on PIPE engine. This PIPE-Sites predictor is here updated through the use of a large high-quality dataset of known PPI sites. Additionally, a similarity-weighted score had been recently developed in PIPE4 and has been proven to be more accurate for the likelihood of PPI prediction. However, PIPE-Sites are shown to be ineffective when applied to similarity-weighted score data. Thus, we here propose and evaluate a new sequence-based PPI site prediction method, named Panorama. This new method leverages similarity-weighted score data to further increase performance over two different performance metrics when evaluated on both <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\boldsymbol{H}$</tex> . sapiens and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\boldsymbol{S}$</tex> , cerevisiae PPI site data.