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PatchSearch: a web server for off-target protein identification

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
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Submitted on : Monday, April 19, 2021 - 8:57:13 AM
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Julien Rey, Ines Rasolohery, Pierre Tuffery, Frederic Guyon, Gautier Moroy. PatchSearch: a web server for off-target protein identification. Nucleic Acids Research, Oxford University Press, 2019, 47 (W1), pp.365-372. ⟨10.1093/nar/gkz478⟩. ⟨hal-03201552⟩



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