ArticleJournal of chemical theory and computation2024
Enhanced and Efficient Predictions of Dynamic Ionization through Constant-pH Adiabatic Free Energy Dynamics.
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 2 papers.
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2 citing papers in PubMed.
- Simultaneous Construction of Free Energy Surfaces via Multisite λ Dynamics and Umbrella Sampling.Journal of chemical theory and computation · 2025Article
- 3D conformation and crystal interaction insights into drug development challenges for HCV drug analogues via molecular simulations.Communications chemistry · 2025Article
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Authors and funding
5 authors.
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Abstract
Dynamic or structurally induced ionization is a critical aspect of many physical, chemical, and biological processes. Molecular dynamics (MD) based simulation approaches, specifically constant pH MD methods, have been developed to simulate ionization states of molecules or proteins under experimentally or physiologically relevant conditions. While such approaches are now widely utilized to predict ionization sites of macromolecules or to study physical or biological phenomena, they are often computationally expensive and require long simulation times to converge. In this article, using the principles of adiabatic free energy dynamics, we introduce an efficient technique for performing constant pH MD simulations within the framework of the adiabatic free energy dynamics (AFED) approach. We call the new approach pH-AFED. We show that pH-AFED provides highly accurate predictions of protein residue p
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