ArticleProteins2011
Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- pH-Dependent Assembly and Stability of Toll-Like Receptor 3/dsRNA Signaling Complex: Insights from Constant pH Molecular Dynamics and Metadynamics Simulations.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- How the pH Controls Photoprotection in the Light-Harvesting Complex of Mosses.Journal of the American Chemical Society · 2023Article
- Effect of pH on stability of dimer structure of the main protease of coronavirus-2.Biophysical chemistry · 2022Article
- Unravelling Constant pH Molecular Dynamics in Oligopeptides with Explicit Solvation Model.Polymers · 2021Article
- Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants.Frontiers in medical technology · 2021Article
- On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides.Polymers · 2020Article
- Article
- Catalytic Site pJournal of chemical information and modeling · 2020Article
- pH-Dependent Protonation of the Phl p 6 Pollen Allergen Studied by NMR and cpH-aMD.Journal of chemical theory and computation · 2019Article
- Reservoir pH replica exchange.The Journal of chemical physics · 2018Article
- Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models.Biophysical journal · 2018Article
- Origin of pKThe journal of physical chemistry. B · 2017Article
- Mimicking titration experiments with MD simulations: A protocol for the investigation of pH-dependent effects on proteins.Scientific reports · 2016Article
- Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.The journal of physical chemistry. B · 2015Article
- Article
- Exploring the role of receptor flexibility in structure-based drug discovery.Biophysical chemistry · 2014Review
- Classical electrostatics for biomolecular simulations.Chemical reviews · 2014Review
- Recent development and application of constant pH molecular dynamics.Molecular simulation · 2014Article
- pKa determination of histidine residues in α-conotoxin MII peptides by 1H NMR and constant pH molecular dynamics simulation.The journal of physical chemistry. B · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
A constant pH molecular dynamics method has been used in the blind prediction of pK(a) values of titratable residues in wild type and mutated structures of the Staphylococcal nuclease (SNase) protein. The predicted values have been subsequently compared to experimental values provided by the laboratory of García-Moreno. CpHMD performs well in predicting the pK(a) of solvent-exposed residues. For residues in the protein interior, the CpHMD method encounters some difficulties in reaching convergence and predicting the pK(a) values for residues having strong interactions with neighboring residues. These results show the need to accurately and sufficiently sample conformational space in order to obtain pK(a) values consistent with experimental results.
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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.