Accuracy of the numerical solution of the Poisson-Boltzmann equation

• Type: Article in International Scientific Journal
• Date: 2005

Authors

Moreira, IS (Author) Other; Fernandes, PA (Author) FCUP; Ramos, MJ (Author) FCUP

Journal

Title: Journal of Molecular Structure: THEOCHEM

Vol. 729

Pages: 11-18

ISSN: 0166-1280

Publisher: Elsevier B.V.

Indexing

ISI Web of Knowledge - 26 Citations

Scopus - 30 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-000-1BC

DOI: 10.1016/j.theochem.2004.12.049

Abstract (EN): Electrostatic interactions and solvation play a relevant role in protein-protein association. The electrostatic solvation free energy can be calculated by solving the Poisson-Boltzmann equation, and new fields of applications of the Poisson-Boltzmann calculations have emerged namely the MMPB/SA (molecular mechanics/Poisson-Boltzmann surface area) methodology to probe protein-protein interactions by calculating free energies. However, the differentiation of the Poisson-Boltzmann equation is only possible, in most cases, using numerical methods, whose accuracy depends on the input parameter set. The study presented here is due to the great importance of a deeper knowledge concerning the influence of parameter variation in solvation free energy. We have investigated the variation of the electrostatic solvation free energy, as well as the computational cost involved, as a function of the variation of key parameters for the numerical differentiation of the Poisson-Boltzmann equation as implemented in DelPhi.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8