3DComplex

Home > PDBe-KB Annotations > 3DComplex

3DComplex

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.

---

Basic Information

What is the FTP URL of the provided annotations (JSON format)?

ftp://ftp.ebi.ac.uk/pub/databases/pdbe-kb/annotations/3DComplex/

What is the URL of the data resource/software?

https://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi

Who is the owner of the data resource/software?

Dr Emmanuel D Levy

What are the annotations provided?

Protein-protein interaction interfaces

How regularly are these annotations updated?

Annually

---

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?

Absolute values are provided

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

There is no confidence score, data is curated

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

There is no confidence score, data is curated

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

Yes, https://shmoo.weizmann.ac.il/elevy/3dcomplexV6/Home.cgi

How are these annotations collected/generated?

Atomic co-ordinates are downloaded from PDB 'Biological Unit'. Quaternary structure annotations, and properties of the interaction surfaces are determined using in-house pipeline of programs.