ArticleThe journal of physical chemistry letters2013
Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.
Article in The journal of physical chemistry letters, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations.Journal of chemical information and modeling · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter.Biophysical journal · 2023Article
- Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals.Nucleic acids research · 2020Article
- Exploring pH Dependent Host/Guest Binding Affinities.The journal of physical chemistry. B · 2020Article
- Predicting Reactive Cysteines with Implicit-Solvent-Based Continuous Constant pH Molecular Dynamics in Amber.Journal of chemical theory and computation · 2020Article
- M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump.Journal of chemical theory and computation · 2017Article
- Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.Biophysical reviews · 2017Review
- Computation of pH-dependent binding free energies.Biopolymers · 2016Review
- Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.PLoS computational biology · 2015Article
- Constant-pH Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulation Method.Journal of chemical theory and computation · 2015Article
- Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.Journal of chemical theory and computation · 2015Article
- pH-dependent transient conformational states control optical properties in cyan fluorescent protein.Journal of the American Chemical Society · 2015Article
- Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.The journal of physical chemistry. B · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.Journal of computational chemistry · 2014Article
- Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.Proteins · 2014Article
- Uncovering pH-dependent transient states of proteins with buried ionizable residues.Journal of the American Chemical Society · 2014Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMD
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Registered trials
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