PDBsum
{{Short description|Pictorial database of 3D structures in the Protein Data Bank}}
{{Infobox biodatabase
|title = PDBSum
|logo = File:Pdbsum logo.gif
|description = Overview of the structures contained within the Protein Data Bank.
|scope = Protein structures
|organism = all
|center = European Bioinformatics Institute (EBI)
|laboratory =
|author = Roman Laskowski & al. (1997)
|pmid = 9433130
|released =
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|url = {{URL|http://www.ebi.ac.uk/pdbsum/}}
|download =
|webservice =
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PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank (PDB).{{cite journal |vauthors = Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM |title = PDBsum: a Web-based database of summaries and analyses of all PDB structures |journal = Trends in Biochemical Sciences |volume = 22 |issue = 12 |pages = 488–90 |date = Dec 1997 |pmid = 9433130 |doi = 10.1016/S0968-0004(97)01140-7 }}{{cite journal |vauthors = Laskowski RA |title = PDBsum: summaries and analyses of PDB structures |journal = Nucleic Acids Research |volume = 29 |issue = 1 |pages = 221–2 |date = Jan 2001 |pmid = 11125097 |pmc = 29784 |doi = 10.1093/nar/29.1.221 }}{{cite journal |vauthors = Laskowski RA, Chistyakov VV, Thornton JM |title = PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids |journal = Nucleic Acids Research |volume = 33 |issue = Database issue |pages = D266-8 |date = Jan 2005 |pmid = 15608193 |pmc = 539955 |doi = 10.1093/nar/gki001 }}{{cite journal |vauthors = Laskowski RA |title = PDBsum new things |journal = Nucleic Acids Research |volume = 37 |issue = Database issue |pages = D355-9 |date = Jan 2009 |pmid = 18996896 |pmc = 2686501 |doi = 10.1093/nar/gkn860 }}
Database
The original version of the database was developed around 1995 by Roman Laskowski and collaborators at University College London.{{cite web |title = PDBsum documentation: About PDBsum |url = https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=doc_about.html |publisher = European Molecular Biology Laboratory – The European Bioinformatics Institute |access-date = 9 September 2014 }} 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.{{cite journal |vauthors = de Beer TA, Berka K, Thornton JM, Laskowski RA |title = PDBsum additions |journal = Nucleic Acids Research |volume = 42 |issue = Database issue |pages = D292-6 |date = Jan 2014 |pmid = 24153109 |pmc = 3965036 |doi = 10.1093/nar/gkt940 }} The RasMol and Jmol molecular graphics software are used to provide a 3D view of molecules and their interactions within PDBsum.
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. PDBsum contains a number of protein structures that 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.{{cite journal |vauthors = 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|author14-link=David S. Wishart |title = DrugBank 3.0: a comprehensive resource for 'omics' research on drugs |journal = Nucleic Acids Research |volume = 39 |issue = Database issue |pages = D1035-41 |date = Jan 2011 |pmid = 21059682 |pmc = 3013709 |doi = 10.1093/nar/gkq1126 }}
See also
References
{{Reflist}}
External links
- {{cite web |url = http://www.ebi.ac.uk/pdbsum/ |title = PDBsum home page |author = Laskowski RA, Thornton JM |publisher = European Bioinformatics Institute }}
Category:Protein structure databases