PDBsum

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PDBSum
Pdbsum logo.gif
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 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 molecular graphics software is 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[edit]

References[edit]

  1. ^ Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (December 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends Biochem. Sci. 22 (12): 488–90. doi:10.1016/S0968-0004(97)01140-7. PMID 9433130. 
  2. ^ Laskowski RA (January 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Res. 29 (1): 221–2. doi:10.1093/nar/29.1.221. PMC 29784. PMID 11125097. 
  3. ^ Laskowski RA, Chistyakov VV, Thornton JM (January 2005). "PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids". Nucleic Acids Res. 33 (Database issue): D266–8. doi:10.1093/nar/gki001. PMC 539955. PMID 15608193. 
  4. ^ Laskowski RA (January 2009). "PDBsum new things". Nucleic Acids Res. 37 (Database issue): D355–9. doi:10.1093/nar/gkn860. PMC 2686501. PMID 18996896. 
  5. ^ a b "PDBsum documentation: About PDBsum". https://www.ebi.ac.uk. Retrieved 9 September 2014. 
  6. ^ a b c de Beer TA, Berka K, Thornton JM, Laskowski RA (2014). "PDBsum additions". Nucleic Acids Res. 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 (8 November 2010). "DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs". Nucleic Acids Research 39 (Database): D1035–D1041. doi:10.1093/nar/gkq1126. PMC 3013709. PMID 21059682. Retrieved 9 September 2014. 

External links[edit]