Covalentizer

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Covalentizer

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/covalentizer/

What is the URL of the data resource/software?

https://covalentizer.weizmann.ac.il/

Who is the owner of the data resource/software?

Nir London

What are the annotations provided?

Candidates for covalent analogues of small molecules

How regularly are these annotations updated?

Weekly

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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?

None

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

Yes, it is RMSD of the maximal common substructure. It is between 0.0-1.5Å, and the lower it is, the higher the confidence level.

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

Yes, it is RMSD of the maximal common substructure. It is between 0.0-1.5Å, and the lower it is, the higher the confidence level.

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

Yes, we benchmarked the method against the structure of covalent kinase inhibitors. It is available in the paper: https://www.biorxiv.org/content/10.1101/2020.09.21.299776v1

How are these annotations collected/generated?

Covalentizer is a computational pipeline for creating irreversible inhibitors, based on X-ray structures of known reversible binders.