 | |
| Content | |
|---|---|
| Description | Overview of the structures contained within theProtein Data Bank. |
| Data types captured | Protein structures |
| Organisms | all |
| Contact | |
| Research center | European Bioinformatics Institute (EBI) |
| Authors | Roman Laskowski & al. (1997) |
| Primary citation | PMID 9433130 |
| Access | |
| Website | www |
| Miscellaneous | |
| Bookmarkable entities | yes |
PDBsum is a database that provides an overview of the contents of each 3Dmacromolecular structure deposited in theProtein Data Bank (PDB).[1][2][3][4]
The original version of the database was developed around 1995 by Roman Laskowski and collaborators atUniversity College London.[5] As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory ofJanet Thornton at theEuropean Bioinformatics Institute (EBI).
Each structure in the PDBsum database includes an image of structure (main view, Bottom view and right view), molecular components contained in the complex(structure), enzyme reaction diagram if appropriate,Gene ontology functional assignments, a 1D sequence annotated byPfam andInterPro domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams ofprotein–protein interactions, analysis of clefts contained within the structure and links to external databases.[6] TheRasMol andJmol molecular graphics software are used to provide a 3D view of molecules and their interactions within PDBsum.[5]
Since the release of the1000 Genomes Project in October 2012, all single amino acid variants identified by the project have been mapped to the corresponding protein sequences in the Protein Data Bank. These variants are also displayed within PDBsum, cross-referenced to the relevantUniProt identifier.[6] PDBsum contains a number ofprotein structures that may be of interest instructure-based drug design. One branch of PDBsum, known as DrugPort, focuses on these models and is linked with theDrugBank drug target database.[6][7]