ArticleJournal of chemical theory and computation2022
Best Practices in Constant pH MD Simulations: Accuracy and Sampling.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
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Who cites it
38 citing papers in PubMed, 77 citations in OpenAlex.
- Membrane environment sets the functional pKBiophysical journal · 2026Article
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Implementation and Validation of Titratable Cysteine in GROMACS-Based Constant-pH Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Mitigating alkaline instability induced by tyrosine-tyrosine repulsion in an FcγRIIIa-binding protein through phenylalanine substitution.Journal of biochemistry · 2026Article
- Mining of natural diversity enables efficient and expressible peptide asparaginyl ligases.Nature communications · 2026Article
- Decoding pH-Driven Phase Transition of Lipid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism.Nature communications · 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
- Constant-pH Simulation of the Human βJournal of chemical information and modeling · 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
- KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1.Molecular cell · 2025Article
- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
- 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
- Protonation State of Active-Site Histidines, Reaction Mechanism and Stereoselectivity in β-Alanine Synthase: A Computational Study.The journal of physical chemistry. B · 2025Article
- A constant pH molecular dynamics and experimental study on the effect of different pH on the structure of urease from Sporosarcina pasteurii.Journal of molecular modeling · 2025Article
- Protonation Effects in Protein-Ligand Complexes - A Case Study of Endothiapepsin and Pepstatin A with Computational and Experimental Methods.ChemMedChem · 2025Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L.
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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.