KinCore

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KinCore

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)?

Not yet available

What is the URL of the data resource/software?

http://dunbrack.fccc.edu/kincore/

Who is the owner of the data resource/software?

Prof. Roland Dunbrack

What are the annotations provided?

Conformational annotations for protein kinase structures

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?

None

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

None

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?

There is no benchmarking in the context of this work.

How are these annotations collected/generated?

The protein kinase structures from PDB are labelled based on the conformation of DFGmotif residues. There are two kinds of labels provided - Spatial label (based on the location of DFG-Phe residue) and Dihedral label (based on conformations of backbone and side-chain dihedrals of DFGmotif residues). The conformation is identified by a distance cutoff criteria from pre-computed cluster centroids. Overall, there are three spatial labels subdivided into a total of eight dihedral labels. The method is described in the article: https://www.pnas.org/content/116/14/6818.abstract