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Article Dans Une Revue Nucleic Acids Research Année : 2019

PatchSearch: a web server for off-target protein identification

Résumé

Abstract The large number of proteins found in the human body implies that a drug may interact with many proteins, called off-target proteins, besides its intended target. The PatchSearch web server provides an automated workflow that allows users to identify structurally conserved binding sites at the protein surfaces in a set of user-supplied protein structures. Thus, this web server may help to detect potential off-target protein. It takes as input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties. It is based on a non-sequential local alignment of the patch over the entire protein surface. Then the PatchSearch web server proposes a ligand binding mode for the potential off-target, as well as an estimated affinity calculated by the Vinardo scoring function. This novel tool is able to efficiently detects potential interactions of ligands with distant off-target proteins. Furthermore, by facilitating the discovery of unexpected off-targets, PatchSearch could contribute to the repurposing of existing drugs. The server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PatchSearch.
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Dates et versions

hal-03824532 , version 1 (15-11-2022)

Identifiants

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Julien Rey, Inès Rasolohery, Pierre Tufféry, Frédéric Guyon, Gautier Moroy. PatchSearch: a web server for off-target protein identification. Nucleic Acids Research, 2019, 47 (W1), pp.W365-W372. ⟨10.1093/nar/gkz478⟩. ⟨hal-03824532⟩
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