AIMC Topic: CRISPR-Associated Protein 9

Clear Filters Showing 1 to 10 of 10 articles

Prime editor with rational design and AI-driven optimization for reverse editing window and enhanced fidelity.

Nature communications Jun 3, 2025
Prime editing (PE) is a precise tool for introducing genetic mutations in eukaryotes. Extending the efficient editing scope and mitigating undesired byproducts are possible. We introduce reverse PE (rPE), a SpCas9-directed variant that enabled DNA ed...
Humans Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Associated Protein 9 Artificial Intelligence CRISPR-Cas Systems HEK293 Cells
View on PubMed DOI

Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Machine Learning Bacterial Proteins RNA Protein Domains Substrate Specificity Francisella Molecular Dynamics Simulation CRISPR-Associated Protein 9 DNA CRISPR-Cas Systems
View on PubMed DOI

Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum.

Journal of chemical information and modeling Jun 5, 2024
The recent development of CRISPR-Cas technology holds promise to correct gene-level defects for genetic diseases. The key element of the CRISPR-Cas system is the Cas protein, a nuclease that can edit the gene of interest assisted by guide RNA. Howeve...
CRISPR-Associated Proteins CRISPR-Associated Protein 9 Machine Learning CRISPR-Cas Systems
View on PubMed DOI

Deep learning models to predict the editing efficiencies and outcomes of diverse base editors.

Nature biotechnology May 15, 2023
Applications of base editing are frequently restricted by the requirement for a protospacer adjacent motif (PAM), and selecting the optimal base editor (BE) and single-guide RNA pair (sgRNA) for a given target can be difficult. To select for BEs and ...
Alkanesulfonic Acids Gene Editing RNA, Guide, CRISPR-Cas Systems Deep Learning CRISPR-Cas Systems CRISPR-Associated Protein 9
View on PubMed DOI

Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases.

Molecular cell May 31, 2022
As part of the ongoing bacterial-phage arms race, CRISPR-Cas systems in bacteria clear invading phages whereas anti-CRISPR proteins (Acrs) in phages inhibit CRISPR defenses. Known Acrs have proven extremely diverse, complicating their identification....
Bacteria CRISPR-Cas Systems Bacteriophages Endonucleases CRISPR-Associated Protein 9 Deep Learning
View on PubMed DOI

Machine-learning approach expands the repertoire of anti-CRISPR protein families.

Nature communications Jul 29, 2020
The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechani...
CRISPR-Associated Protein 9 Host-Parasite Interactions Sequence Homology, Amino Acid Sequence Analysis, Protein CRISPR-Cas Systems Datasets as Topic Gene Editing Machine Learning Archaea Bacteria Bacteriophages Computational Biology Viral Proteins
View on PubMed DOI

SpCas9 activity prediction by DeepSpCas9, a deep learning-based model with high generalization performance.

Science advances Nov 6, 2019
We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing single-guide RNA-encoding and target sequence pairs. Deep learning-based training on this large dataset of SpCas9-indu...
Gene Editing RNA, Guide, CRISPR-Cas Systems CRISPR-Associated Protein 9 Mutation Internet Reproducibility of Results Deep Learning Humans CRISPR-Cas Systems
View on PubMed DOI

Predictable and precise template-free CRISPR editing of pathogenic variants.

Nature Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
DNA Repair K562 Cells Alleles Menkes Kinky Hair Syndrome CRISPR-Associated Protein 9 HEK293 Cells Reproducibility of Results Humans Templates, Genetic HCT116 Cells Hermanski-Pudlak Syndrome Substrate Specificity Base Sequence Fibroblasts Machine Learning Gene Editing CRISPR-Cas Systems
View on PubMed DOI

Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR-Cas9 off-target activity.

NAR genomics and bioinformatics Jun 1, 2025
Despite advances in determining the factors influencing cleavage activity of a CRISPR-Cas9 single guide RNA (sgRNA) at an (off-)target DNA sequence, a comprehensive assessment of pertinent physico-chemical/structural descriptors is missing. In partic...
RNA, Guide, CRISPR-Cas Systems CRISPR-Associated Protein 9 Mutation Gene Editing Machine Learning CRISPR-Cas Systems
View on PubMed DOI

Machine learning predicts new anti-CRISPR proteins.

Nucleic acids research May 21, 2020
The increasing use of CRISPR-Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that...
Machine Learning Proteome Bacterial Proteins Streptococcus Sequence Analysis, Protein CRISPR-Associated Protein 9 Prophages
View on PubMed DOI
Popular Topics
Recent Journals