PDBsum is a database that provides an overview of the contents of each 3D
macromolecular structure deposited in the
Protein Data Bank.
The original version of the database was developed around 1995 by Roman Laskowski and collaborators at
University College London.
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
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families.
Uses
...
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.
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
The 1000 Genomes Project (abbreviated as 1KGP), launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists planned to sequence the genomes of at least one th ...
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
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activ ...
. One branch of PDBsum, known as DrugPort, focuses on these models and is linked with the
DrugBank drug target database.
See also
*
Crystallographic database
*
Protein structure
*
Protein structure database
References
External links
* {{cite web , url = http://www.ebi.ac.uk/pdbsum/ , title = PDBsum home page , author = Laskowski RA, Thornton JM , publisher = European Bioinformatics Institute
Biological databases
Science and technology in Cambridgeshire
South Cambridgeshire District