Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

pH-Dependent Dynamics of Complex RNA Macromolecules

(2013) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids

(2013) Garrett B. Goh et al.   Journal of Physical Chemistry Letters

pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

(2013) Sean M. Law et al.   PROTEIN SCIENCE

Role of pKa of Nucleobases in the Origins of Chemical Evolution

(2012) Ramanarayanan Krishnamurthy   ACCOUNTS OF CHEMICAL RESEARCH

Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

(2012) Jason A. Wallace et al.   JOURNAL OF CHEMICAL PHYSICS

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

(2012) Jason M. Swails et al.   Journal of Chemical Theory and Computation

pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method

(2012) Danial Sabri Dashti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

(2012) Jason A. Wallace et al.   Journal of Physical Chemistry Letters

Charged Nucleobases and Their Potential for RNA Catalysis

(2011) Jennifer L. Wilcox et al.   ACCOUNTS OF CHEMICAL RESEARCH

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

(2011) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies

(2011) Jennifer L. Knight et al.   Journal of Chemical Theory and Computation

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

(2011) Jason A. Wallace et al.   Journal of Chemical Theory and Computation

Applying efficient implicit nongeometric constraints in alchemical free energy simulations

(2011) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Probing pH-Dependent Dissociation of HdeA Dimers

(2011) Bin W. Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Arginine residues at internal positions in a protein are always charged

(2011) M. J. Harms 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

Progress in the prediction of pKa values in proteins

(2011) Emil Alexov 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

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

(2011) Jens E. Nielsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

(2010) Jana K. Shen   BIOPHYSICAL JOURNAL

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

(2010) Sarah L. Williams et al.   Journal of Chemical Theory and Computation

Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

(2010) Yilin Meng et al.   Journal of Chemical Theory and Computation

pH-Dependent Interactions Guide the Folding and Gate the Transmembrane Pore of the β-Barrel Membrane Protein OmpG

(2010) Mehdi Damaghi et al.   JOURNAL OF MOLECULAR BIOLOGY

Constant-pH Molecular Dynamics Simulations Reveal a β-Rich Form of the Human Prion Protein

(2010) Sara R. R. Campos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modulation of Buried Ionizable Groups in Proteins with Engineered Surface Charge

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

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

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Downhill versus Barrier-Limited Folding of BBL 1: Energetic and Structural Perturbation Effects upon Protonation of a Histidine of Unusually Low pKa

(2008) Eyal Arbely et al.   JOURNAL OF MOLECULAR BIOLOGY

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Acidic range titration of HEWL using a constant-pH molecular dynamics method

(2008) Miguel Machuqueiro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS