GAPIN: Grouped and Aligned Protein Interface Networks

Abstract

SummaryGAPIN is a web-based application for structural interaction network analysis among any type of PDB molecules, regardless of whether their interfaces are between chain-chain or chain-ligand. A special emphasis is given to graph clustering, allowing users to scrutinize target contexts for ligand candidates. We show how GAPIN can be used to unveil underlying hydrophobic patterns on a set of peptidase-inhibitor complexes. In another experiment, we show there is a positive correlation between cluster sizes and the presence of druggable spots, indicating that the clustering may discriminate the higher complexity of these hot subnetworks.\n\nAvailability and implementationGAPIN is freely available as an easy-to-use web interface at https://gapin.unifei.edu.br.\n\nContactbiharck@ufmg.br, carlos.silveira@unifei.edu.br.\n\nSupplementary informationSupplementary data are available online.