ReviewCurrent opinion in structural biology2022
Constant pH molecular dynamics simulations: Current status and recent applications.
Review in Current opinion in structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
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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
46 citing papers in PubMed.
- A Multi-Scale Computational Framework for Anti-Persister Tuberculosis Drug Discovery.Chemical biology & drug design · 2026Review
- pH-Sensitive Amino Lipid-Driven Pore Formation Enables Endosomal Escape of Lipid Nanoparticles.Nature communications · 2026Article
- Molecular Origins of pH Gradients in Charge-Regulated Biomolecular Condensates.bioRxiv : the preprint server for biology · 2026Article
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Molecular Modeling of N-Acetylglucosamine Binding to the I154R Mutant of NAGLU: Pathogenic Insights into Sanfilippo Syndrome Type B.International journal of molecular sciences · 2026Article
- A Sequence-Specific Theory for Charge-Regulating IDPs.The journal of physical chemistry. B · 2026Article
- Improving the Estimation of pThe journal of physical chemistry. B · 2026Article
- Protein Electrostatic Properties are Finetuned Through Evolution.bioRxiv : the preprint server for biology · 2026Article
- pH-Driven βACS omega · 2026Article
- TrIPP: a trajectory iterative pKa predictor.Bioinformatics (Oxford, England) · 2026Article
- Machine learning for enzyme catalytic activity: current progress and future horizons.Briefings in bioinformatics · 2026Review
- Article
- GPU-Accelerated Implementation of Constant-pH Molecular Dynamics in NAMD.Journal of chemical information and modeling · 2025Article
- Structure-Based Modeling of Environment-Dependent Protonation States Across LNP Formulations with Atomistic CpHMD.Molecular pharmaceutics · 2025Article
- Permeation enhancer-induced membrane defects assist the oral absorption of peptide drugs.Nature communications · 2025Article
- Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.Journal of chemical information and modeling · 2025Article
- Charge Neutralization During Peptide Transport in the Bacterial SecYEG Translocon.Biomolecules · 2025Article
- Revealing pH-dependent antimicrobial peptide, GL13K, characteristics: A constant pH molecular dynamics study.bioRxiv : the preprint server for biology · 2025Article
- Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.PLoS computational biology · 2025Article
- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Many important protein functions are carried out through proton-coupled conformational dynamics. Thus, the ability to accurately model protonation states dynamically has wide-ranging implications. Over the past two decades, two main types of constant pH methods (discrete and continuous) have been developed to enable proton-coupled molecular dynamics (MD) simulations. In this short review, we discuss the current status of the development and highlight recent applications that have advanced our understanding of protein structure-function relationships. We conclude the review by outlining the remaining challenges in the method development and projecting important areas for future applications.
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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.