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bioRxiv · 10.1101/498923

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

Laville, P.·Martin, J.·Launay, G.·Regad, L.·Camproux, A.-C.·de Vries, S.·Petitjean, M.
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Abstract

MotivationThe 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.\n\nResultsWe 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 [A], or 3.6 [A] for a set of 18 PR2-ligand interfaces. We found at most 17 contact residues with PR2 ligands.\n\nAvailabilityFree binaries and documentation are available through a software repository located at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html\n\nContactpetitjean.chiral@gmail.com, michel.petitjean@univ-paris-diderot.fr

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Laville, P., Martin, J., Launay, G., Regad, L., Camproux, A.-C., de Vries, S., Petitjean, M.. 2018-12-18. A non-parametric method to compute protein-protein and protein-ligands interfaces. Application to HIV-2 protease-inhibitors complexes. https://doi.org/10.1101/498923

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