title: Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase.
abstract: We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three-dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D-RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI-272 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39-0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is extremely useful for examining multiple specific solvent-solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.
authors.affiliation: Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Sindhikara
authors.forename: Norio
authors.initials: N
authors.lastname: Yoshida
authors.forename: Fumio
authors.initials: F
authors.lastname: Hirata
mesh_terms: D000465:Algorithms; D016333:HIV Protease / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D006180:Proton-Translocating ATPases / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*
chemical_list: D009842:Oligopeptides; D012997:Solvents; D016333:HIV Protease; D006180:Proton-Translocating ATPases; C077822:kynostatin 272