ArticleNucleic acids research2019
KnotProt 2.0: a database of proteins with knots and other entangled structures.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Tied to Work: Topologically Knotted SPOUT Methyltransferases and UCH Deubiquitinases in Cellular Biochemistry.Journal of cellular biochemistry · 2026Review
- Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.Nature communications · 2026Article
- 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
- Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data.bioRxiv : the preprint server for biology · 2026Article
- Peptide cages: bioinspired supramolecular architectures for next-generation applications.Chemical science · 2026Review
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Phosphoglycerate Kinase Can Adopt Topologically Misfolded Forms That Are More Stable Than Its Native State.Journal of the American Chemical Society · 2026Article
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Properties Governing Native State Entanglements and Relationships to Protein Function.Journal of molecular biology · 2025Article
- Folding and knotting of biotic and prebiotic amino acid sequences through reverse evolution.Biophysical journal · 2025Article
- Geometry based prediction of tau protein sites and motifs associated with misfolding and aggregation.Scientific reports · 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
- Knot data analysis using multiscale Gauss link integral.Proceedings of the National Academy of Sciences of the United States of America · 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
- Non-covalent Lasso Entanglements in Folded Proteins: Prevalence, Functional Implications, and Evolutionary Significance.Journal of molecular biology · 2024Article
- Making topological protein links using enzymatic reactions.National science review · 2024Article
- Structure, dynamics, and stability of the smallest and most complex 7The Journal of biological chemistry · 2024Article
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9 authors.
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Abstract
The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).
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