A non-parametric method to compute protein–protein and protein–ligands interfaces. Application to HIV-2 protease–inhibitors complexes

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Laville, Pierre | Martin, Juliette | Launay, Guillaume | Regad, Leslie | Camproux, Anne-Claude | de Vries, Sjoerd | Petitjean, Michel

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biorXiv paper ; DOI 10.1101/498923 ; https://doi.org/10.1101/498923 ;https://www.biorxiv.org/content/10.1101/498923v1. Motivation The accurate description of interfaces is needed to identify which residues interact with another molecule or macromolecule. In addition, a data structure is required to compare interfaces within or between families of protein–protein or protein–ligands complexes. In order to avoid many unwanted comparisons, we looked for a parameter free computation of interfaces. This need appeared at the occasion of bioinformatics studies by our research team focusing on HIV-2 protease (PR2) resistance to its inhibitors.Results We designed the PPIC software (Protein Protein Interface Computation). It offers three methods of computation of interfaces: (1) our original parameter free method, (2) the Voronoi tessellation approach, and (3) the cutoff distance method. For the latter, we suggest on the basis of 1050 dimers protein–protein interfaces that the optimal cutoff distance is 3.7 Å, or 3.6 Å for a set of 18 PR2–ligand interfaces. We found at most 17 contact residues with PR2 ligands.Availability Free binaries and documentation are available through a software repository located at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.htmlContact petitjean.chiral{at}gmail.com, michel.petitjean{at}univ-paris-diderot.fr

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