ArticleJournal of chemical theory and computation2013
pH-dependent dynamics of complex RNA macromolecules.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.Nucleic acids research · 2024Article
- Understanding the adsorption of plasmid DNA and RNA molecules onto arginine-agarose chromatographic resin.Molecular biology reports · 2022Article
- Exploring pH Dependent Host/Guest Binding Affinities.The journal of physical chemistry. B · 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
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function.ACS omega · 2019Article
- Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.Journal of chemical theory and computation · 2017Article
- Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.Biophysical reviews · 2017Review
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology.Nanomedicine : nanotechnology, biology, and medicine · 2017Article
- All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.Journal of chemical theory and computation · 2016Article
- Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.Journal of the American Chemical Society · 2016Article
- 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
- Membrane environment modulates the pKa values of transmembrane helices.The journal of physical chemistry. B · 2015Article
- pH-dependent transient conformational states control optical properties in cyan fluorescent protein.Journal of the American Chemical Society · 2015Article
- Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations.Biochemistry · 2015Article
- Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.The journal of physical chemistry. B · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The role of pH-dependent protonation equilibrium in modulating RNA dynamics and function is one of the key unanswered questions in RNA biology. Molecular dynamics (MD) simulations can provide insight into the mechanistic roles of protonated nucleotides, but it is only capable of modeling fixed protonation states and requires prior knowledge of the key residue's protonation state. Recently, we developed a framework for constant pH molecular dynamics simulations (CPHMD
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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.