AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

Internet* ; Software* ; Databases, Protein* ; Models, Molecular* ; Protein Conformation* ; Algorithms*; Proteins/chemistry ; Protein Folding ; Computer Graphics

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/.
(© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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UMO-2018/31/B/NZ1/04016 Narodowe Centrum Nauki

0 (Proteins)

Date Created: 20240606 Date Completed: 20240704 Latest Revision: 20240706

20250114

PMC11223836

10.1093/nar/gkae443

38842945