ArticleJournal of chemical theory and computation2024
Constant-pH Simulations with the Polarizable Atomic Multipole AMOEBA Force Field.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Structure-Based Modeling of Environment-Dependent Protonation States Across LNP Formulations with Atomistic CpHMD.Molecular pharmaceutics · 2025Article
- Constant-pH Simulation of the Human βJournal of chemical information and modeling · 2025Article
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.Journal of chemical theory and computation · 2025Article
- Enhanced and Efficient Predictions of Dynamic Ionization through Constant-pH Adiabatic Free Energy Dynamics.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Accurately predicting protein behavior across diverse pH environments remains a significant challenge in biomolecular simulations. Existing constant-pH molecular dynamics (CpHMD) algorithms are limited to fixed-charge force fields, hindering their application to biomolecular systems described by permanent atomic multipoles or induced dipoles. This work overcomes these limitations by introducing the first polarizable CpHMD algorithm in the context of the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field. Additionally, our implementation in the open-source Force Field X (FFX) software has the unique ability to handle titration state changes for crystalline systems including flexible support for all 230 space groups. The evaluation of constant-pH molecular dynamics (CpHMD) with the AMOEBA force field was performed on 11 crystalline peptide systems that span the titrating amino acids (Asp, Glu, His, Lys, and Cys). Titration states were correctly predicted for 15 out of the 16 amino acids present in the 11 systems, including for the coordination of Zn
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Registered trials
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