ArticleThe journal of physical chemistry. B2025
Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD.
Article in The journal of physical chemistry. B, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed.
- A Multi-Scale Computational Framework for Anti-Persister Tuberculosis Drug Discovery.Chemical biology & drug design · 2026Review
- pH-Driven βACS omega · 2026Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
This tutorial examines the application of constant-pH molecular dynamics simulations, a method that addresses the critical problem of modeling systems that can adopt multiple protonation states. While conventional molecular dynamics simulations generally assume fixed protonation states, using a constant-pH technique actively explores dynamic shifts in protonation as the simulation progresses. Once completed, constant-pH simulations can be analyzed to yield titration curves that can be readily compared to experiment.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.