ArticleJournal of chemical information and modeling2018
Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis.
Article in Journal of chemical information and modeling, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Precision Chemistry for Protein Lysine Modification.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications.Journal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pJournal of chemical theory and computation · 2025Article
- KaMLs for Predicting Protein pbioRxiv : the preprint server for biology · 2025Article
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- QM/MM Simulations of Afatinib-EGFR Addition: The Role of β-Dimethylaminomethyl Substitution.Journal of chemical theory and computation · 2024Article
- Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2024Article
- phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.Journal of chemical information and modeling · 2024Article
- Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease.Journal of chemical information and modeling · 2023Article
- Analysis of the ERK Pathway Cysteinome for Targeted Covalent Inhibition of RAF and MEK Kinases.Journal of chemical information and modeling · 2023Article
- An Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease.bioRxiv : the preprint server for biology · 2023Article
- Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.Frontiers in molecular biosciences · 2023Article
- Increasing the Realism ofJournal of chemical theory and computation · 2022Article
- Extending the Stochastic Titration CpHMD to CHARMM36m.The journal of physical chemistry. B · 2022Article
- Scalable Constant pH Molecular Dynamics in GROMACS.Journal of chemical theory and computation · 2022Article
- A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven pJournal of chemical theory and computation · 2022Article
- Article
- Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases.Journal of medicinal chemistry · 2022Article
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Authors and funding
3 authors.
Funding
Abstract
Solution pH plays an important role in structure and dynamics of biomolecular systems; however, pH effects cannot be accurately accounted for in conventional molecular dynamics simulations based on fixed protonation states. Continuous constant pH molecular dynamics (CpHMD) based on the λ-dynamics framework calculates protonation states on the fly during dynamical simulation at a specified pH condition. Here we report the CPU-based implementation of the CpHMD method based on the GBNeck2 generalized Born (GB) implicit-solvent model in the pmemd engine of the Amber molecular dynamics package. The performance of the method was tested using pH replica-exchange titration simulations of Asp, Glu and His side chains in 4 miniproteins and 7 enzymes with experimentally known p K
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