title: Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution.
abstract: The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: theblobbysurface, an implicit Gaussian atom centered surface, and theskinsurface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege theskinto theblobbysurface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of theskinsurface in Poisson-Boltzmann calculations with the DelPhi solver. Results indicate that theskinand Connolly surfaces have a comparable performance from this last point of view.
authors.affiliation: Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Decherchi
authors.forename: José
authors.initials: J
authors.lastname: Colmenares
authors.forename: Chiara Eva
authors.initials: CE
authors.lastname: Catalano
authors.forename: Michela
authors.initials: M
authors.lastname: Spagnuolo
authors.forename: Emil
authors.initials: E
authors.lastname: Alexov
authors.forename: Walter
authors.initials: W
authors.lastname: Rocchia
keywords: Blobby Surface; Connolly Surface; Molecular Surface; Poisson-Boltzmann; Skin Surface