AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites |
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| Authors: | Arina Afanasyeva Sergey Izmailov Michel Grigoriev Michael Petukhov |
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| Affiliation: | 1. Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Saint‐Petersburg, Russia;2. Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Leningrad district, Russia;3. Department of computational physics, Saint‐Petersburg State University, Russia;4. Laboratory of Molecular Biology of Eucaryotes (LBME) UMR 5099 CNRS, Toulouse, France;5. Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri |
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| 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. © 2015 Wiley Periodicals, Inc. |
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| Keywords: | structural water molecular docking ATPase |
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