POPScomp

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POPScomp

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/POPScomp_PDBML/

What is the URL of the data resource/software?

http://popscomp.org:3838

Who is the owner of the data resource/software?

Fraternali Lab, King's College London

What are the annotations provided?

Solvent Accessible Surface Areas (SASAs) of atoms, residues, chains and molecules.

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; surface areas; lower limit 0, no upper limit; Angstrom squared

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

The benchmarked values are overall 5% for all-atom structures and 10% for low-resolution structures [Calpha (protein), phosphate (DNA)]. To be on the conservative side, we report confidence of 0.9 throughout.

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

We set the confidence_level to 'high', because the overall error has been benchmarked. In future releases more detailed error estimates could be built into the method.

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

Bemchmarking has been performed during method development. Yes, in Table 1 of the primary publication ([DOI: 10.1093/nar/gkg601](DOI: 10.1093/nar/gkg601)).

How are these annotations collected/generated?

The POPS program estimates the shielding of an atom's surface area by neighbouring atoms within the same molecule (protein or DNA/RNA), i.e. [1,2;1,3;1,4]-bonded neighbours or non-bonded neighbours [>1,4]. The estimate is based on a geometric formula that takes into account the atom type and the relevant atom-pair distances. The POPS program outputs solvent-accessible solvent areas of atoms, residues, chains and molecules for a given solvent radius (water = 1.4 A).