Scalable Constant pH Molecular Dynamics in GROMACS

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

(2022) Pavel Buslaev et al.   Journal of Chemical Theory and Computation

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

(2020) Gerrit Groenhof et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides

(2020) Plamen Dobrev et al.   Journal of Chemical Theory and Computation

Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber

(2020) Robert C. Harris et al.   Journal of Chemical Theory and Computation

Backmapping triangulated surfaces to coarse-grained membrane models

(2020) Weria Pezeshkian et al.   Nature Communications

Titratable Martini model for constant pH simulations

(2020) Fabian Grünewald et al.   JOURNAL OF CHEMICAL PHYSICS

pH-Dependent Conformational Changes Lead to a Highly Shifted pKa for a Buried Glutamic Acid Mutant of SNase

(2020) Ankita Sarkar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

(2019) Ankita Sarkar et al.   JOURNAL OF PHYSICAL CHEMISTRY B

GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations

(2019) Robert C. Harris et al.   Journal of Chemical Information and Modeling

Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis

(2018) Yandong Huang et al.   Journal of Chemical Information and Modeling

Reservoir pH replica exchange

(2018) Ana Damjanovic et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer

(2016) Serena Donnini et al.   Journal of Chemical Theory and Computation

Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations

(2016) Plamen Dobrev et al.   Journal of Chemical Theory and Computation

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

(2016) Yandong Huang et al.   Journal of Chemical Theory and Computation

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

pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition

(2015) Christopher R. Ellis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion

(2015) Xiancheng Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria

(2015) M. Olivia Kim 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

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

(2014) Wei Chen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Recent development and application of constant pH molecular dynamics

(2014) Wei Chen et al.   MOLECULAR SIMULATION

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

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

(2013) Ludovic Sauguet et al.   EMBO JOURNAL

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

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

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

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

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

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

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

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

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

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

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology