1. GAPIN: Grouped and Aligned Protein Interface Networks
- Author
-
de Melo-Minardi Rc, Sabrina de A. Silveira, da Silveira Ch, Coelho Al, Romanelli Jpr, and Araújo Bm
- Subjects
Set (abstract data type) ,Interaction network ,Computer science ,Protein Data Bank (RCSB PDB) ,Druggability ,Cluster (physics) ,Data mining ,User interface ,Cluster analysis ,computer.software_genre ,computer ,Clustering coefficient - 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.Availability and implementationGAPIN is freely available as an easy-to-use web interface at https://gapin.unifei.edu.br.Contactbiharck@ufmg.br, carlos.silveira@unifei.edu.br.Supplementary informationSupplementary data are available online.
- Published
- 2019
- Full Text
- View/download PDF