ArticleMethods in enzymology2015
Multiscale methods for computational RNA enzymology.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
11 citing papers in PubMed, 20 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme.ACS catalysis · 2019Article
- Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme.RNA (New York, N.Y.) · 2019Article
- Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology.ACS catalysis · 2019Article
- An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.ACS chemical biology · 2019Article
- Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.The journal of physical chemistry. B · 2019Article
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.The Journal of chemical physics · 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
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
RNA catalysis is of fundamental importance to biology and yet remains ill-understood due to its complex nature. The multidimensional "problem space" of RNA catalysis includes both local and global conformational rearrangements, changes in the ion atmosphere around nucleic acids and metal ion binding, dependence on potentially correlated protonation states of key residues, and bond breaking/forming in the chemical steps of the reaction. The goal of this chapter is to summarize and apply multiscale modeling methods in an effort to target the different parts of the RNA catalysis problem space while also addressing the limitations and pitfalls of these methods. Classical molecular dynamics simulations, reference interaction site model calculations, constant pH molecular dynamics (CpHMD) simulations, Hamiltonian replica exchange molecular dynamics, and quantum mechanical/molecular mechanical simulations will be discussed in the context of the study of RNA backbone cleavage transesterification. This reaction is catalyzed by both RNA and protein enzymes, and here we examine the different mechanistic strategies taken by the hepatitis delta virus ribozyme and RNase A.
Indexed as
Identifiers
What OpenQuestion holds
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.