ArticleProtein science : a publication of the Protein Society2022
AlphaFold predicts the most complex protein knot and composite protein knots.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 3Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.Nucleic acids research · 2025Article
- LassoPred: a tool to predict the 3D structure of lasso peptides.Nature communications · 2025Article
- Folding of a tandemly knotted protein: Evidence that a polypeptide chain can get out of deep kinetic traps.Protein science : a publication of the Protein Society · 2025Article
- Eco-friendly nano colloids for enhanced black gram (Vigna mungo) seed viability: experimental and computational analysis.BMC plant biology · 2025Article
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 2024Article
- Theta-curves in proteins.Protein science : a publication of the Protein Society · 2024Article
- AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.Nucleic acids research · 2024Article
- Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.Protein science : a publication of the Protein Society · 2024Article
- When Machine Learning Meets 2D Materials: A Review.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Structure, dynamics, and stability of the smallest and most complex 7The Journal of biological chemistry · 2024Article
- AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Topological links in predicted protein complex structures reveal limitations of AlphaFold.Communications biology · 2023Article
- De novo design of knotted tandem repeat proteins.Nature communications · 2023Article
- AlphaFold predicts novel human proteins with knots.Protein science : a publication of the Protein Society · 2023Article
- Application of artificial scaffold systems in microbial metabolic engineering.Frontiers in bioengineering and biotechnology · 2023Review
- Are there double knots in proteins? Prediction andFrontiers in molecular biosciences · 2023Article
- A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these predictions for cases where the protein backbone exhibits rare topological complexity, that is, knotting. Amongst others, we discovered a 7
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