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EMBL-EBI Protein Data Bank in Europe (PDBe)

Hinxton, UK

General information

PDBe is a founding member of the Worldwide Protein Data Bank, the organisation that manages the single worlwide archive of macromolecular structures  - The Protein Data Bank (PDB). The wwPDB partners collaborate on deposition and annotation of atomic models of structures deposited to the PDB. These include structures determined using X-ray crystallography, nuclear magnetic resonance spectroscopy and 3D electron cryo-microscopy, whereas the asscociated 3D-EM volume maps are deposited to EMDB which is also managed by PDBe. The two archives contain a large number of macromolecular complexes and many macromolecule-ligand complexes. Recently PDBe also started an archive for raw image data, EMPIAR, related to the EM data in EMDB. Support for additional imaging modalities is gradually being added to EMPIAR.

 

Expertise

The team has expertise in managing macromolecular and cellular structure data and works closely with the structural biology community and continues to develop PDB, EMDB and EMPIAR data archives to meet user demands. The team has expert structural biologists, chemists and software engineers and has an active outreach and training program. We work closely with other biomedical data resources and have established major data resources to address data integration so as to enrich the information available for macromolecular structures.

 

Technologies offered for the Open Call

- Advanced tools and services to analyse macromolecular structure data including PISA, which
  annotates the probable quaternary structure for X-ray crystallographic entries
- Data-integration resource SIFTS (developed in collaboration with UniProt), able to enrich the
  annotations available for both macromolecular structures and protein sequences
- PDBeShape - a shape matching server (developed in collaboration with STFC) that enables the
  searching of EMDB and PDB based on the shape of assemblies and complexes

 

Additional resources offered for the Open Call

- Tools to identify the macromolecular complexes and related data available in PDB and EMDB,
  including ranking to denote "best" available structure for a given complex.
- Provision of additional value-added information for the macromolecular complexes available in
  other biomedical data resources basedon the SIFTS and PDBe data resources; this includes cross-
  references to other major data resources, the molecular properties of the complex (interface
  residues, buried surface area), etc. 

 

Access modalities

The search facility and data pertaining to a specific entry will be made available via the PDBe REST API so it can be accessed programmatically. These data are also made  available via web interfaces. We are also happy to hold training sessions or have users on-site and work with them to meet their needs in identifying appropriate data.  

 

Scientific and technical requirements

A well-defined requirement (e.g., a particular macromolecular complex or target compound that binds a particular complex) that can be translated into a search query to identify data of interest from the database.

 

Contacts

Scientific contact: Sameer Velankar, Ardan Patwardhan
Technical contact: Aleks Gutmanas, Saqib Mir, John Berrisford

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