@ARTICLE{Afanasyeva20151973,
author={Afanasyeva, A. and Izmailov, S. and Grigoriev, M. and Petukhov, M.},
title={AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites},
journal={Journal of Computational Chemistry},
year={2015},
volume={36},
number={26},
pages={1973-1977},
doi={10.1002/jcc.24022},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-84941055115&doi=10.1002%2fjcc.24022&partnerID=40&md5=9671042d23952f7578ea3a68548318eb},
affiliation={Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, Leningrad district, 188300, Russian Federation; Department of Computational Physics, Saint-Petersburg State University, Peterhof, Botanikaya 64/2198504, Russian Federation; Laboratory of Molecular Biology of Eucaryotes (LBME) UMR 5099 CNRS, Toulouse, France; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO, United States},
abstract={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. AquaBridge is a tool for seeking structural water molecules within protein binding pockets, developed as a module for the ICM-Pro software package for molecular modeling. This utility is based on Monte Carlo energy minimization algorithms and selects the water molecule conformations that can form "water bridges" by calculating the values of the total energy of a modeled water molecule and of the number of hydrogen bonds that it can form between the target protein and the ligand. © 2015 Wiley Periodicals, Inc.},
author_keywords={ATPase;  molecular docking;  structural water},
correspondence_address1={Afanasyeva, A.; Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Russian Federation},
publisher={John Wiley and Sons Inc.},
issn={01928651},
coden={JCCHD},
pubmed_id={26339759},
language={English},
abbrev_source_title={J. Comput. Chem.},
document_type={Article},
source={Scopus},
}

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This utility is based on Monte Carlo energy minimization algorithms and selects the water molecule conformations that can form \"water bridges\" by calculating the values of the total energy of a modeled water molecule and of the number of hydrogen bonds that it can form between the target protein and the ligand. © 2015 Wiley Periodicals, Inc.},\r\nauthor_keywords={ATPase; molecular docking; structural water},\r\ncorrespondence_address1={Afanasyeva, A.; Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Russian Federation},\r\npublisher={John Wiley and Sons Inc.},\r\nissn={01928651},\r\ncoden={JCCHD},\r\npubmed_id={26339759},\r\nlanguage={English},\r\nabbrev_source_title={J. Comput. 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