ArticleLiving journal of computational molecular science2022
A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0].
Article in Living journal of computational molecular science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Biomolecular Condensates Act as Distinct Solvation Environments That Reshape Amino Acid pJournal of the American Chemical Society · 2026Article
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- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.Cell reports. Physical science · 2025Article
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- pH-Dependent Assembly and Stability of Toll-Like Receptor 3/dsRNA Signaling Complex: Insights from Constant pH Molecular Dynamics and Metadynamics Simulations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases.Protein science : a publication of the Protein Society · 2024Article
- Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality.Nature communications · 2024Article
- Role of Protonation States in the Stability of Molecular Dynamics Simulations of High-Resolution Membrane Protein Structures.The journal of physical chemistry. B · 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
- In Silico Identification of Lead Compounds for Pseudomonas Aeruginosa PqsA Enzyme: Computational Study to Block Biofilm Formation.Biomedicines · 2023Article
- GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.Journal of chemical theory and computation · 2022Article
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Authors and funding
6 authors.
Funding
Abstract
Like temperature and pressure, solution pH is an important environmental variable in biomolecular simulations. Virtually all proteins depend on pH to maintain their structure and function. In conventional molecular dynamics (MD) simulations of proteins, pH is implicitly accounted for by assigning and fixing protonation states of titratable sidechains. This is a significant limitation, as the assigned protonation states may be wrong and they may change during dynamics. In this tutorial, we guide the reader in learning and using the various continuous constant pH MD methods in Amber and CHARMM packages, which have been applied to predict p
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