title: A morphometric approach for the accurate solvation thermodynamics of proteins and ligands.
abstract: We have developed a versatile method for calculating solvation thermodynamic quantities for molecules, starting from their atomic coordinates. The contribution of each atom to the thermodynamic quantities is estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem, and the coefficients reflecting their solvation properties. This treatment enables us to calculate the solvation free energy with high accuracy despite of the limited computational load. The method can readily be applied to macromolecules in an all-atom molecular model, allowing the stability of these molecules' structures in solution to be evaluated.
authors.affiliation: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. yharano@protein.osaka-u.ac.jp
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Harano
authors.forename: Roland
authors.initials: R
authors.lastname: Roth
authors.forename: Shuntaro
authors.initials: S
authors.lastname: Chiba
mesh_terms: D056004:Molecular Dynamics Simulation; D000442:Octanols / Q000737:chemistry; D055550:Protein Stability; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D000442:Octanols; D011506:Proteins; D012997:Solvents; D014867:Water
keywords: Hadwiger's theorem; hydration; ligand binding; protein stability; solvation thermodynamics