The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins

Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins

(2011) Ana Damjanović et al.   JOURNAL OF PHYSICAL CHEMISTRY A

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

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

(2011) Evan J. Arthur et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein electrostatics and pKa blind predictions; contribution from empirical predictions of internal ionizable residues

(2011) Mats H. M. Olsson   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Developing hybrid approaches to predict pKa values of ionizable groups

(2011) Shawn Witham et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Calculation of pKa in proteins with the microenvironment modulated-screened coulomb potential

(2011) Jufang Shan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease

(2011) M. R. Gunner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Histidine in continuum electrostatics protonation state calculations

(2011) Vernon Couch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

(2011) Arieh Warshel et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress in the prediction of pKa values in proteins

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

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions

(2011) Wenli Meng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

(2011) Miguel Machuqueiro 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

Electrostatic pKa computations in proteins: Role of internal cavities

(2011) Tim Meyer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind, one-eyed, or eagle-eyed? pKa calculations during blind predictions with staphylococcal nuclease

(2011) Paul Czodrowski   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol

(2011) Yifan Song   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

(2011) Sarah L. Williams et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method

(2011) Jim Warwicker   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Estimating the pKa values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem

(2011) Gisela D. Cymes et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

On the development of protein pKa calculation algorithms

(2011) Tommy Carstensen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

(2011) Savvas Polydorides et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface

(2011) Daniel L. Ensign et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

(2011) Jason A. Wallace et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease

(2010) Daniel A. Karp et al.   BIOCHEMISTRY

Modulation of Buried Ionizable Groups in Proteins with Engineered Surface Charge

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

Charges in the hydrophobic interior of proteins

(2010) D. G. Isom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Remeasuring HEWL pKa values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pKa calculations

(2010) Helen Webb et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study

(2008) Ana Damjanović et al.   BIOPHYSICAL JOURNAL

Crystallographic Study of Hydration of an Internal Cavity in Engineered Proteins with Buried Polar or Ionizable Groups

(2008) Jamie L. Schlessman et al.   BIOPHYSICAL JOURNAL

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein

(2008) Ana Damjanović et al.   Journal of Chemical Information and Modeling

Benchmarking pKaPrediction Methods for Residues in Proteins

(2008) Courtney L. Stanton et al.   Journal of Chemical Theory and Computation

Electrostatic Effects in a Network of Polar and Ionizable Groups in Staphylococcal Nuclease

(2008) Kelli L. Baran et al.   JOURNAL OF MOLECULAR BIOLOGY

pKaof Residue 66 inStaphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling

(2008) Nilanjan Ghosh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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