WEBnm@

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WEBnm@

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/webNMA/

What is the URL of the data resource/software?

http://apps.cbu.uib.no/webnma3/

Who is the owner of the data resource/software?

Nathalie Reuter

What are the annotations provided?

Flexibility prediction in the form of the normalized displacement of each amino acid in the structure. The displacement is predicted by performing Normal mode analysis (NMA) using an elastic network model (ENM) on each single PDB file. Note that only the first 200 lowest-frequency normal modes are used to calculate the displacement.

How regularly are these annotations updated?

Bi-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?

Yes. The “raw_score” represents the prediction of the residue flexibility, and it is a normalized value so that the sum over all residues is equal to 100, thus the value range is from 0 to 100. It does not have a unit.

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?

No. Note, however, there is “confidence_classification” provided with value “null”, which is required by the agreed JSON schema (https://gitlab.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-schema/-/blob/master/funpdbe_schema.json commit: 5cbda944)

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

We do not have benchmarking datasets so far.

How are these annotations collected/generated?

The data is generated first by running our tool WEBnma against each PDB file downloaded from PDBe(rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/pdb/). For the successfully processed PDBs, the result is then converted to the agreed JSON format, and finally verified by the validator(https://gitlab.ebi.ac.uk/pdbe-kb/funpdbe/funpdbe-validator, commit: 97eab72b). The total number of valid JSON files was about 157,000 collected from 169633 downloaded PDBs.