Improving the desolvation penalty in empirical protein pK_a modeling

TY - JOUR

T1 - Improving the desolvation penalty in empirical protein pKa modeling

AU - Olsson, Mats Henrik Mikael

PY - 2012/3

Y1 - 2012/3

N2 - 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.

AB - 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.

U2 - 10.1007/s00894-011-1141-1

DO - 10.1007/s00894-011-1141-1

M3 - Journal article

C2 - 21670992

SN - 1610-2940

VL - 18

SP - 1097

EP - 1106

JO - Journal of Molecular Modeling

JF - Journal of Molecular Modeling

IS - 3

ER -