Reservoir pH replica exchange

Anomalous Properties of Lys Residues Buried in the Hydrophobic Interior of a Protein Revealed with 15N-Detect NMR Spectroscopy

(2018) Christos M. Kougentakis et al.   Journal of Physical Chemistry Letters

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

(2017) Brian K. Radak et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

(2017) Zhi Yue et al.   Journal of Chemical Theory and Computation

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations

(2016) A. Sofia F. Oliveira et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water

(2016) Xiongwu Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Activation of a Transmembrane Proton Channel from Constant pH Molecular Dynamics

(2016) Wei Chen et al.   Journal of Physical Chemistry Letters

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

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

(2016) Yandong Huang et al.   Nature Communications

Interpretation of pH–Activity Profiles for Acid–Base Catalysis from Molecular Simulations

(2015) Thakshila Dissanayake et al.   BIOCHEMISTRY

Conformational Reorganization Coupled to the Ionization of Internal Lys Residues in Proteins

(2015) Daniel E. Richman et al.   BIOCHEMISTRY

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method

(2015) Juyong Lee et al.   Journal of Chemical Theory and Computation

Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone

(2015) Logan S. Ahlstrom et al.   JOURNAL OF MOLECULAR BIOLOGY

pH-Dependent Transient Conformational States Control Optical Properties in Cyan Fluorescent Protein

(2015) Elena N. Laricheva et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

(2015) Xiongwu Wu et al.   PLoS Computational Biology

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Underlying Thermodynamics of pH-Dependent Allostery

(2014) Natali V. Di Russo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

(2014) Eric R. May et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues

(2014) Garrett B. Goh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates

(2013) W.F. Drew Bennett et al.   CANADIAN JOURNAL OF CHEMISTRY

Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method

(2013) Asim Okur et al.   Journal of Chemical Theory and Computation

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

(2013) Garrett B. Goh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A pH-dependent coarse-grained model for peptides

(2013) Marta Enciso et al.   Soft Matter

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

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Rapid Calculation of Protein pKa Values Using Rosetta

(2012) Krishna Praneeth Kilambi et al.   BIOPHYSICAL JOURNAL

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

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

Structural Reorganization Triggered by Charging of Lys Residues in the Hydrophobic Interior of a Protein

(2012) Michael S. Chimenti et al.   STRUCTURE

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

(2012) Natali V. Di Russo et al.   PLoS Computational Biology

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini 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

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

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   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

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

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

Structural Origins of High Apparent Dielectric Constants Experienced by Ionizable Groups in the Hydrophobic Core of a Protein

(2010) Michael S. Chimenti et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

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

(2008) Ana Damjanović et al.   BIOPHYSICAL JOURNAL

CHARMMing: A New, Flexible Web Portal for CHARMM

(2008) Benjamin T. Miller et al.   Journal of Chemical Information and Modeling

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