ReviewMethods (San Diego, Calif.)2009
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
Review in Methods (San Diego, Calif.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Recent Advances in Elucidating the Mechanism of the NADPH-Cytochrome P450 Reductase-Mediated Electron Transfer Cycle: Experimental and Computational Perspectives.Molecules (Basel, Switzerland) · 2025Review
- Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction.Journal of the American Chemical Society · 2024Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.Journal of structural biology · 2019Review
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- Molecular insight on the non-covalent interactions between carbapenems and L,D-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study.Journal of computer-aided molecular design · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.Journal of chemical theory and computation · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.The Journal of chemical physics · 2015Article
- Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.Biopolymers · 2015Article
- The energy landscape of adenylate kinase during catalysis.Nature structural & molecular biology · 2015Article
- Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.Journal of the American Chemical Society · 2015Article
- The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.Physical chemistry chemical physics : PCCP · 2015Article
- Computational evidence for structural consequences of kiteplatin damage on DNA.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2015Article
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.Nucleic acids research · 2014Article
- Molecular modeling of nucleic acid structure: energy and sampling.Current protocols in nucleic acid chemistry · 2013Review
- Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.Journal of the American Chemical Society · 2013Article
- DFT investigations of phosphotriesters hydrolysis in aqueous solution: a model for DNA single strand scission induced by N-nitrosoureas.Journal of molecular modeling · 2013Article
Corrections and comments
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5 authors.
Funding
Abstract
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.
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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.