ChannelsDB

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ChannelsDB

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/ChannelsDB/

What is the URL of the data resource/software?

http://ncbr.muni.cz/ChannelsDB

Who is the owner of the data resource/software?

Radka Svobodova Varekova

What are the annotations provided?

Information about residues that are lining ligand-accessible-pathways referred to as channels. Channels connect active sites that are deeply buried in the structure with the surface enabling trafficking substrate/products of enzymatic reactions as well as Additionally, they facilitate and control the transport action of water, ions and other molecules across biomembranes.

How regularly are these annotations updated?

Annually

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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?

yes. there are 3 main sources of channel annotation. "curated" refers to channels that were manually curated and crosschecked with a published papers. We are confident about the biological relevance of these channels. "high" refers to channels leading to a subset of known cofactors in enzyme structures and pores that spans lipid bilayer. These channels are mostly biologically relevant, but as this is fully automated process we cannot guarantee that all of them are meaningful. "medium" refers to channels that leads to active sites annotated in the Catalytic Site Atlas. This resource uses both manually curated and computationally inferred active sites, so the accuracy of these channels is lower.

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

We have a list of structures that we used for the method development. The list can be found here: https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-5-39

How are these annotations collected/generated?

Manual annotations come from the manual annotation of students involved in the projects as well as deposited by authors of the scientific papers that used Mole online service. Automatic annotations for cofactor channels and pores are extracted using the same method without manual intervention.