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AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites
Author(s) -
Afanasyeva Arina,
Izmailov Sergey,
Grigoriev Michel,
Petukhov Michael
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24022
Subject(s) - in silico , docking (animal) , chemistry , molecule , active site , ligand (biochemistry) , protein ligand , binding site , computational biology , small molecule , protein–ligand docking , computational chemistry , combinatorial chemistry , molecular dynamics , virtual screening , biochemistry , biology , enzyme , organic chemistry , medicine , receptor , nursing , gene
We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small‐molecule ligands. We tested its efficiency on a representative set of human ATP‐binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein–ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design. © 2015 Wiley Periodicals, Inc.