title: Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.
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 electrostaic 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 developmental 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.
authors.affiliation: Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Piazzale Kolbe, 4, Udine 33100, Italy. federico.fogolari@uniud.it
authors.forename: Federico
authors.initials: F
authors.lastname: Fogolari
authors.forename: Alessandra
authors.initials: A
authors.lastname: Corazza
authors.forename: Vijaylakshmi
authors.initials: V
authors.lastname: Yarra
authors.forename: Anusha
authors.initials: A
authors.lastname: Jalaru
authors.forename: Paolo
authors.initials: P
authors.lastname: Viglino
authors.forename: Gennaro
authors.initials: G
authors.lastname: Esposito
mesh_terms: D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry*; D012984:Software; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D011506:Proteins