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

Federico Fogolari, Alessandra Corazza, Vijaylakshmi Yarra, Anusha Jalaru, Paolo Viglino, Gennaro Esposito

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article numberS18
JournalBMC bioinformatics
Volume13
Issue numberSUPPL.4
DOIs
StatePublished - Mar 28 2012

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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