Conformational sampling and polarization of Asp26 in pK a calculations of thioredoxin

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

(2018) Samuel C. Gill et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease

(2018) Jinfeng Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

(2018) Maximiliano Riquelme et al.   Journal of Chemical Information and Modeling

Extensive Assessment of Various Computational Methods for Aspartate’s pKa Shift

(2017) Zhaoxi Sun et al.   Journal of Chemical Information and Modeling

Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations

(2017) Hanwool Yoon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Amino acid residues adjacent to the catalytic cavity of tetramer l -asparaginase II contribute significantly to its catalytic efficiency and thermostability

(2016) Shuiqing Long et al.   ENZYME AND MICROBIAL TECHNOLOGY

Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1

(2016) Esteban Vöhringer-Martinez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The effect of the environment on the methyl transfer reaction mechanism between trimethylsulfonium and phenolate

(2016) David Adrian Saez et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Microscopic mechanisms that govern the titration response and pK a values of buried residues in staphylococcal nuclease mutants

(2016) Yuqing Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Contemporary NMR Studies of Protein Electrostatics

(2015) Mathias A.S. Hass et al.   Annual Review of Biophysics

A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation

(2015) David Adrian Saez et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protonation/deprotonation process of Emodin in aqueous solution and pKa determination: UV/Visible spectrophotometric titration and quantum/molecular mechanics calculations

(2014) Antonio R. da Cunha et al.   CHEMICAL PHYSICS

An Overview of Electrostatic Free Energy Computations for Solutions and Proteins

(2014) Yen-Lin Lin et al.   Journal of Chemical Theory and Computation

All-atom polarizable force field for DNA based on the classical drude oscillator model

(2014) Alexey Savelyev et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Influence of Ser-154, Cys-113, and the Phosphorylated Threonine Residue on the Catalytic Reaction Mechanism of Pin1

(2014) Esteban Vöhringer-Martinez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

(2013) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting

(2013) Steven K. Burger et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Developing hybrid approaches to predict pKa values of ionizable groups

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

The ORCA program system

(2011) Frank Neese   Wiley Interdisciplinary Reviews-Computational Molecular Science

Structure, Function, and Mechanism of Thioredoxin Proteins

(2010) Jean-Francois Collet et al.   ANTIOXIDANTS & REDOX SIGNALING

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Ionizable Groups: pKValues and Their Contribution to Protein Stability and Solubility

(2009) C. Nick Pace et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Electrostatic Potentials from Self-Consistent Hirshfeld Atomic Charges

(2009) Sofie Van Damme et al.   Journal of Chemical Theory and Computation

Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

(2009) Jozef Hritz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin

(2008) Changge Ji et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B