New Features

Integrating PDB Data with NIH Common Fund Data Resources

07/21

RCSB PDB has integrated three-dimensional structural information with 3 new resources that fall under the umbrella of the NIH Common Fund Data Resources. Ultimately, this integration is expected to enable investigation of novel biological questions, and promote a more complete understanding of human health and disease.

Relevant PDB structures are now linked to individual data in PHAROS, GTEx, and IMPC.

  • PHAROS is part of the Integrating the Druggable Genome (IDG) project and presents integrated data for 3 of the most important drug target protein families: GPCRs, ion channels and kinases. Some of the data types it covers include: disease, phenotypic and ontologies such as the Drug Target Ontology.
  • GTEx is a public resource for the study of tissue-specific gene expression and regulation.
  • IMPC covers data related to mouse phenotypes, as part of an international effort by 19 research institutions to identify the function of every protein-coding gene in the mouse genome.

Data are accessible from individual Structure Summary pages and Advanced Search.

<a href="https://www.rcsb.org/structure/6VIE">The Structure Summary page for PDB structure 6vie (Structure of caspase-1 in complex with gasdermin D) links to corresponding pages at PHAROS and GTEx for Entities 1 and 2, and to IMPC for Entity 3. </a>The Structure Summary page for PDB structure 6vie (Structure of caspase-1 in complex with gasdermin D) links to corresponding pages at PHAROS and GTEx for Entities 1 and 2, and to IMPC for Entity 3.
Searching PDB entries that have a mapping to these 3 NIH Common Fund data resources is possible in the <a href="http://www.rcsb.org/search/advanced">RCSB.org Advanced Search User Interface</a> by selecting Attribute: <I>Linked External Resources</i> and <i>UniProt-mapped Resource</i>.Searching PDB entries that have a mapping to these 3 NIH Common Fund data resources is possible in the RCSB.org Advanced Search User Interface by selecting Attribute: Linked External Resources and UniProt-mapped Resource.

This work was supported by an NIH Common Fund Data Use Award intended for Enhancing Utility and Usage of Common Fund Data Sets.