Dataset Information

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 http://bioserv.rpbs.univ-paris-diderot.fr/services/PatchSearch.

SUBMITTER: Rey J

PROVIDER: S-EPMC6602448 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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PatchSearch: a web server for off-target protein identification.

Rey Julien J Rasolohery Inès I Tufféry Pierre P Guyon Frédéric F Moroy Gautier G

Nucleic acids research 20190701 W1

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 with ...[more]

PMID: 31131411

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Dataset Information

PatchSearch: a web server for off-target protein identification.

Publications

PatchSearch: a web server for off-target protein identification.

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