Highly accurate biomolecular electrostatics in continuum dielectric environments
Implicit solvent models based on the Poisson-Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson-Boltzmann solver is developed based on the matched interface and boundary (MIB) method, w...
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 29(2008), 1 vom: 15. Jan., Seite 87-97 |
|---|---|
| 1. Verfasser: | |
| Weitere Verfasser: | , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2008
|
| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. |
| Zusammenfassung: | Implicit solvent models based on the Poisson-Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson-Boltzmann solver is developed based on the matched interface and boundary (MIB) method, which rigorously enforces the continuity conditions of both the electrostatic potential and its flux at the molecular surface. The MIB based PB solver attains much better convergence rates as a function of mesh size compared to conventional finite difference and finite element based PB solvers. Consequently, highly accurate electrostatic potentials and solvation energies are obtained at coarse mesh sizes. In the context of biomolecular electrostatic calculations it is demonstrated that the MIB method generates substantially more accurate solutions of the PB equation than other established methods, thus providing a new level of reference values for such models. Initial results also indicate that the MIB method can significantly improve the quality of electrostatic surface potentials of biomolecules that are frequently used in the study of biomolecular interactions based on experimental structures |
|---|---|
| Beschreibung: | Date Completed 12.03.2008 Date Revised 21.11.2008 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |