PDBsum

PDBSum
Content
Description Overview of the structures contained within the Protein 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.ebi.ac.uk/pdbsum/
Tools
Miscellaneous
Bookmarkable entities yes

PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank.[1][2][3][4] The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London.[5] As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of Janet Thornton at the European 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 by Pfam and InterPro domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams of protein-protein interactions, analysis of clefts contained within the structure and links to external databases.[6] The RasMol and Jmol molecular graphics software are used to provide a 3D view of molecules and their interactions within PDBsum.[5]

Since the release of the 1000 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 relevant UniProt identifier.[6] PDBsum contains a number of protein structures which may be of interest in structure-based drug design. One branch of PDBsum, known as DrugPort, focuses on these models and is linked with the DrugBank drug target database.[6][7]

See also

References

  1. ↑ Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (Dec 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends in Biochemical Sciences 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7. PMID 9433130.
  2. ↑ Laskowski RA (Jan 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Research 29 (1): 221–2. doi:10.1093/nar/29.1.221. PMC 29784. PMID 11125097.
  3. ↑ Laskowski RA, Chistyakov VV, Thornton JM (Jan 2005). "PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids". Nucleic Acids Research 33 (Database issue): D266–8. doi:10.1093/nar/gki001. PMC 539955. PMID 15608193.
  4. ↑ Laskowski RA (Jan 2009). "PDBsum new things". Nucleic Acids Research 37 (Database issue): D355–9. doi:10.1093/nar/gkn860. PMC 2686501. PMID 18996896.
  5. 1 2 "PDBsum documentation: About PDBsum". European Molecular Biology Laboratory – The European Bioinformatics Institute. Retrieved 9 September 2014.
  6. 1 2 3 de Beer TA, Berka K, Thornton JM, Laskowski RA (Jan 2014). "PDBsum additions". Nucleic Acids Research 42 (Database issue): D292–6. doi:10.1093/nar/gkt940. PMC 3965036. PMID 24153109.
  7. ↑ Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs". Nucleic Acids Research 39 (Database issue): D1035–41. doi:10.1093/nar/gkq1126. PMC 3013709. PMID 21059682.

External links

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