ReviewCurrent opinion in structural biology2022
Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods.
Review in Current opinion in structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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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.
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Who cites it
17 citing papers in PubMed.
- CRISPR RNA architecture steers Cas9 catalysis and fidelity via a guide repeat clasp motif.Nucleic acids research · 2026Article
- Molecular mechanisms and biotechnology applications of CRISPR-Cas12a.Nature reviews. Molecular cell biology · 2026Review
- Article
- Characterization and modulation of human insulin degrading enzyme conformational dynamics to control enzyme activity.bioRxiv : the preprint server for biology · 2025Article
- A guide RNA repeat checkpoint steers CRISPR-Cas9 catalysis.bioRxiv : the preprint server for biology · 2025Article
- Molecular Docking as a Key Driver of Biocontrol for Agri-Food Security.Biotech (Basel (Switzerland)) · 2025Review
- Graph Attention Neural Networks Reveal TnsC Filament Assembly in a CRISPR-Associated Transposon.bioRxiv : the preprint server for biology · 2025Article
- Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation.Biochemistry · 2025Article
- Graph theory approaches for molecular dynamics simulations.Quarterly reviews of biophysics · 2024Article
- Probing Electrostatic Interactions in DNA-Bound CRISPR/Cas9 Complexes by Molecular Dynamics Simulations.ACS omega · 2024Article
- Cas12a domain flexibility guides R-loop formation and forces RuvC resetting.Molecular cell · 2024Article
- An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a.Nature communications · 2024Article
- Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease.Biophysical journal · 2023Article
- A Perspective on Sustainable Computational Chemistry Software Development and Integration.Journal of chemical theory and computation · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- The Electronic Structure of Genome Editors from the First Principles.Electronic structure (Bristol, England) · 2023Article
- Full-Length Model of SaCas9-sgRNA-DNA Complex in Cleavage State.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) genome-editing revolution established the beginning of a new era in life sciences. Here, we review the role of state-of-the-art computations in the CRISPR-Cas9 revolution, from the early refinement of cryo-EM data to enhanced simulations of large-scale conformational transitions. Molecular simulations reported a mechanism for RNA binding and the formation of a catalytically competent Cas9 enzyme, in agreement with subsequent structural studies. Inspired by single-molecule experiments, molecular dynamics offered a rationale for the onset of off-target effects, while graph theory unveiled the allosteric regulation. Finally, the use of a mixed quantum-classical approach established the catalytic mechanism of DNA cleavage. Overall, molecular simulations have been instrumental in understanding the dynamics and mechanism of CRISPR-Cas9, contributing to understanding function, catalysis, allostery, and specificity.
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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.