World Library  
Flag as Inappropriate
Email this Article

PDBsum

Article Id: WHEBN0031070840
Reproduction Date:

Title: PDBsum  
Author: World Heritage Encyclopedia
Language: English
Subject: Carbohydrate-binding module, Cobalamin biosynthesis, Protease inhibitor (biology), DNA clamp, Cupin superfamily
Collection: Biological Databases
Publisher: World Heritage Encyclopedia
Publication
Date:
 

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 //pdbsum.uk.ac.ebiwww
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

References

  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.  
  2. ^ Laskowski RA (January 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Res. 29 (1): 221–2.  
  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.  
  4. ^ Laskowski RA (January 2009). "PDBsum new things". Nucleic Acids Res. 37 (Database issue): D355–9.  
  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.  
  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.  

External links

  • Laskowski RA, Thornton JM. "PDBsum home page". European Bioinformatics Institute. 
This article was sourced from Creative Commons Attribution-ShareAlike License; additional terms may apply. World Heritage Encyclopedia content is assembled from numerous content providers, Open Access Publishing, and in compliance with The Fair Access to Science and Technology Research Act (FASTR), Wikimedia Foundation, Inc., Public Library of Science, The Encyclopedia of Life, Open Book Publishers (OBP), PubMed, U.S. National Library of Medicine, National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health (NIH), U.S. Department of Health & Human Services, and USA.gov, which sources content from all federal, state, local, tribal, and territorial government publication portals (.gov, .mil, .edu). Funding for USA.gov and content contributors is made possible from the U.S. Congress, E-Government Act of 2002.
 
Crowd sourced content that is contributed to World Heritage Encyclopedia is peer reviewed and edited by our editorial staff to ensure quality scholarly research articles.
 
By using this site, you agree to the Terms of Use and Privacy Policy. World Heritage Encyclopedia™ is a registered trademark of the World Public Library Association, a non-profit organization.
 


Copyright © World Library Foundation. All rights reserved. eBooks from Project Gutenberg are sponsored by the World Library Foundation,
a 501c(4) Member's Support Non-Profit Organization, and is NOT affiliated with any governmental agency or department.