KnotProt

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KnotProt

This page provides a description of the annotations provided by this PDBe-KB Consortium Member. These annotations are available via public FTP, from the PDBe graph database, the PDBe graph API, and on the PDBe-KB aggregated views of proteins.

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Basic Information

What is the FTP URL of the provided annotations (JSON format)?

ftp://ftp.ebi.ac.uk/pub/databases/pdbe-kb/annotations/KnotProt/

What is the URL of the data resource/software?

https://knotprot.cent.uw.edu.pl/

Who is the owner of the data resource/software?

Joanna Sulkowska

What are the annotations provided?

The database provides information regarding the presence of knots or slipknots on protein chains and, in the case of their presence, also the type of the knot/slipknot and its position in the chain.

How regularly are these annotations updated?

Monthly

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Description of the data

Is there a "raw_score" provided? How to interpret it? Does it have a value range? Does it have a unit?

Yes. Although our principal method of the assessment of the presence of knots is probabilistic, the data is manually revised before publishing, so when publishing the data to PDBe-KB we give it a value of 1.0 if we identify a knot/slipknot at a given position in the protein chain. For more detailed data, in particular, the raw probability values, please refer to the KnotProt database entry.

Is there a "confidence_score" provided? How to interpret it? Does it have a value range?

Yes. Similarly, to the value of the "raw_score", it may only contain the value 1.0 for a given position in the protein chain when we identify a knot/slipknot after a manual revision of the raw data in the KnotProt database.

Is there a "confidence_level" provided? How is it decided?

None

Are there benchmarking datasets? Are they available publicly? If yes, what is the URL?

No, not at this moment.

How are these annotations collected/generated?

"The KnotProt 2.0 database collects information about entangled proteins, i.e. proteins which form knots, slipknots, and knotoids. Such structures are defined in either probabilistic, or deterministic (based on disulfide or ion bonds) way. The KnotProt 2.0 database classifies all such proteins, represents their entire complexity in the form of a “knotting fingerprint” and presents many biological and geometrical statistics based on these results. The KnotProt database verifies not only if a given chain is knotted (or not), but it also analyzes all subchains of a given chain. This means that for a chain of length N, we analyze all subchains spanned between atoms (aminoacids) k and l (with 1 ≤ k < l ≤ N). For a given protein this information is presented in the database within the panel “Knotting data”, in the form of an interactive “knotting fingerprint” (matrix diagram). The implementations of algorithms (in particular, the principle one: the Alexander polynomial) used to detect knots and slipknots are contained in our recently published Python package: Topoly (https://topoly.cent.uw.edu.pl/). New protein chains published in the PDBe database are processed every week automatically. The raw data is manually revised periodically and only then becomes available. "