期刊
NUCLEIC ACIDS RESEARCH
卷 47, 期 W1, 页码 W365-W372出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkz478
关键词
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资金
- Agence Nationale de la Recherche [ANR-IA-2011-IFB [ANR-11-INSB-0013]]
- INSERM [U1133]
- Universite Paris Diderot
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.univparis-diderot.fr/services/PatchSearch.
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