ArticleNucleic acids research2015
KnotProt: a database of proteins with knots and slipknots.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
- Chemoenzymatic Modification of Microcin J25 with Single-Residue Precision Provides New-to-Nature Lasso Peptides.JACS Au · 2026Article
- Knotted folds induced by homochiral all-parallel (or all-antiparallel) double-helices.PNAS nexus · 2026Article
- Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants.The journal of physical chemistry. B · 2026Article
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants.bioRxiv : the preprint server for biology · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- Effects of Knotting on the Collapse of Active Ring Polymers.Macromolecules · 2025Article
- Link node: A method to characterize the chain topology of intrinsically disordered proteins.Quantitative biology (Beijing, China) · 2025Article
- Khovanov Laplacian and Khovanov Dirac for knots and links.Journal of physics. Complexity · 2025Article
- The protein-protein interaction between two spliced leadermicroPublication biology · 2025Article
- Activity-driven polymer knotting for macromolecular topology engineering.Science advances · 2024Article
- Knot data analysis using multiscale Gauss link integral.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- 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
- IDRWalker: A Random Walk Based Tool for Generating Intrinsically Disordered Regions in Large Protein Complexes.ACS omega · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
- Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance.Journal of molecular biology · 2024Article
- Evolutionary Khovanov homology.AIMS mathematics · 2024Article
- The SKMT Algorithm: A method for assessing and comparing underlying protein entanglement.PLoS computational biology · 2023Article
26 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.
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