title: MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.
abstract: One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.
authors.affiliation: Department of Physics and Astronomy, The University of Texas at San Antonio, TX 78249, USA.
authors.forename: Sandra
authors.initials: S
authors.lastname: Vergara-Perez
authors.affiliation: Department of Physics and Astronomy, The University of Texas at San Antonio, TX 78249, USA.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Marucho
keywords: Graphical user interface; Matlab software; Poisson-Boltzmann equation; biomolecular electrostatic calculations; mean electrostatic potential