ArticleNucleic acids research2024
AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- Zika virus recruits karyopherin α6 for efficient replication via NS2B.Journal of virology · 2026Article
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- 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
- Native entanglement misfolding contributes to age-associated structural changebioRxiv : the preprint server for biology · 2026Article
- AlphaLasso-a web server to identify loop and lasso motifs in 3D structure of biopolymers.Nucleic acids research · 2025Article
- LassoPred: a tool to predict the 3D structure of lasso peptides.Nature communications · 2025Article
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5 authors.
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Abstract
The availability of 3D protein models is rapidly increasing with the development of structure prediction algorithms. With the expanding availability of data, new ways of analysis, especially topological analysis, of those predictions are becoming necessary. Here, we present the updated version of the AlphaKnot service that provides a straightforward way of analyzing structure topology. It was designed specifically to determine knot types of the predicted structure models, however, it can be used for all structures, including the ones solved experimentally. AlphaKnot 2.0 provides the user's ability to obtain the knowledge necessary to assess the topological correctness of the model. Both probabilistic and deterministic knot detection methods are available, together with various visualizations (including a trajectory of simplification steps to highlight the topological complexities). Moreover, the web server provides a list of proteins similar to the queried model within AlphaKnot's database and returns their knot types for direct comparison. We pre-calculated the topology of high-quality models from the AlphaFold Database (4th version) and there are now more than 680.000 knotted models available in the AlphaKnot database. AlphaKnot 2.0 is available at https://alphaknot.cent.uw.edu.pl/.
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