This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

Federico Fogolari12*, Alessandra Corazza12, Vijaylakshmi Yarra1, Anusha Jalaru1, Paolo Viglino12 and Gennaro Esposito12

Author Affiliations

1 Dipartimento di Scienze Mediche e Biologiche. Università di Udine, Piazzale Kolbe, 4, Udine 33100, Italy

2 Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d'Oro 305, Roma 00136, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S18  doi:10.1186/1471-2105-13-S4-S18

Published: 28 March 2012

Abstract

Background

The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for the more fundamental approach based on the Poisson-Boltzmann equation, and allows estimation of pairwise contributions to electrostatic effects in the molecular context.

Results

We have implemented in a single program most common analyses of the electrostatic properties of proteins. The program first computes generalized Born radii, via a surface integral and then it uses generalized Born radii (using a finite radius test particle) to perform electrostic analyses. In particular the ouput of the program entails, depending on user's requirement:

1) the generalized Born radius of each atom;

2) the electrostatic solvation free energy;

3) the electrostatic forces on each atom (currently in a dvelopmental stage);

4) the pH-dependent properties (total charge and pH-dependent free energy of folding in the pH range -2 to 18;

5) the pKa of all ionizable groups;

6) the electrostatic potential at the surface of the molecule;

7) the electrostatic potential in a volume surrounding the molecule;

Conclusions

Although at the expense of limited flexibility the program provides most common analyses with requirement of a single input file in PQR format. The results obtained are comparable to those obtained using state-of-the-art Poisson-Boltzmann solvers. A Linux executable with example input and output files is provided as supplementary material.