Recent development and application of constant pH molecular dynamics

Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

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

The pH-Triggered Conversion of the PrPc to PrPsc

(2013) Guo-Ping Zhou et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

pH-Dependent Dynamics of Complex RNA Macromolecules

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

pKa Determination of Histidine Residues in α-Conotoxin MII Peptides by 1H NMR and Constant pH Molecular Dynamics Simulation

(2013) Owen M. McDougal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations

(2013) Diogo Vila-Viçosa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids

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

Deconstructing Activation Events in Rhodopsin

(2013) Elena N. Laricheva et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characterizing the Protonation State of Cytosine in Transient G·C Hoogsteen Base Pairs in Duplex DNA

(2013) Evgenia N. Nikolova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-Assembly and Bilayer–Micelle Transition of Fatty Acids Studied by Replica-Exchange Constant pH Molecular Dynamics

(2013) Brian H. Morrow et al.   LANGMUIR

Chaperone activation by unfolding

(2013) L. Foit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A pH-dependent coarse-grained model for peptides

(2013) Marta Enciso et al.   Soft Matter

The N-terminal domains of spider silk proteins assemble ultrafast and protected from charge screening

(2013) Simone Schwarze et al.   Nature Communications

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

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

(2012) Brian H. Morrow et al.   JOURNAL OF CHEMICAL PHYSICS

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

Reversibility of Prion Misfolding: Insights from Constant-pH Molecular Dynamics Simulations

(2012) Diogo Vila-Viçosa et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Fine-Tuning the pH Trigger of Self-Assembly

(2012) Arijit Ghosh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Structural basis for proton conduction and inhibition by the influenza M2 protein

(2012) Mei Hong et al.   PROTEIN SCIENCE

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

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

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

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

(2011) Yuhang Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effects of Two Solvent Conditions on the Free Energy Landscape of the BBL Peripheral Subunit Binding Domain

(2011) Hanzhong Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulating pH Titration of a Single Surfactant in Ionic and Nonionic Surfactant Micelles

(2011) Brian H. Morrow et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   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

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

Essentials for ATP Synthesis by F1F0ATP Synthases

(2009) Christoph von Ballmoos et al.   Annual Review of Biochemistry

CHARMM: The biomolecular simulation program

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

pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

(2009) Jason M. Swails et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evidence for a Catalytic Dyad in the Active Site of Homocitrate Synthase fromSaccharomyces cerevisiae†

(2008) Jinghua Qian et al.   BIOCHEMISTRY

Multidrug efflux transporter, AcrB—the pumping mechanism

(2008) S MURAKAMI   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent advances in implicit solvent-based methods for biomolecular simulations

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

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