title: Analysis of biomolecular solvation sites by 3D-RISM theory.
abstract: We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.
authors.affiliation: Department of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Sindhikara
authors.forename: Fumio
authors.initials: F
authors.lastname: Hirata
mesh_terms: D000465:Algorithms; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000201:enzymology; D006801:Humans; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012997:Solvents; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1