AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites.
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.
Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russia.|Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, Leningrad district, 188300, Russia.
Arina
A
Afanasyeva
Department of computational physics, Saint-Petersburg State University, Peterhof, Botanikaya 64/2, 198504, Russia.
Sergey
S
Izmailov
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, Missouri.
Michel
M
Grigoriev
Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russia.|Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Orlova Roscha, Gatchina, Leningrad district, 188300, Russia.
Michael
M
Petukhov
D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain / Q000502:physiology*; D003198:Computer Simulation; D006801:Humans; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D002352:Carrier Proteins; D011506:Proteins; D014867:Water
ATPase; molecular docking; structural water