title: Improving the desolvation penalty in empirical protein pKa modeling.
abstract: Unlike atomistic and continuum models, empirical pk(a) predicting methods need to include desolvation contributions explicitly. This study describes a new empirical desolvation method based on the Born solvation model. The new desolvation model was evaluated by high-level Poisson-Boltzmann calculations, and discussed and compared with the current desolvation model in PROPKA-one of the most widely used empirical protein pK(a) predictors. The new desolvation model was found to remove artificial erratic behavior due to discontinuous jumps from man-made first-shell cutoffs, and thus improves the desolvation description significantly.
authors.affiliation: Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark. Mats.Olsson@hotmail.com
authors.forename: Mats H M
authors.initials: MH
authors.lastname: Olsson
mesh_terms: D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents
chemical_list: D011506:Proteins; D012997:Solvents