pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants

(2016) Lin Wang et al.   Communications in Computational Physics

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function

(2013) Lin Li et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

Protonation and pK changes in protein–ligand binding

(2013) Alexey V. Onufriev et al.   QUARTERLY REVIEWS OF BIOPHYSICS

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

Large shifts in pKa values of lysine residues buried inside a protein

(2011) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values

(2011) J. Michael Word et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modulation of Buried Ionizable Groups in Proteins with Engineered Surface Charge

(2010) Angel L. Pey et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular determinants of the pKavalues of Asp and Glu residues in staphylococcal nuclease

(2009) Carlos A. Castañeda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High tolerance for ionizable residues in the hydrophobic interior of proteins

(2008) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme

(2004) Jim Warwicker   PROTEIN SCIENCE