PDBsum

Database

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 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 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.

References

References

1. (Dec 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures". Trends in Biochemical Sciences.
2. (Jan 2001). "PDBsum: summaries and analyses of PDB structures". Nucleic Acids Research.
3. (Jan 2005). "PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids". Nucleic Acids Research.
4. (Jan 2009). "PDBsum new things". Nucleic Acids Research.
5. "PDBsum documentation: About PDBsum". European Molecular Biology Laboratory – The European Bioinformatics Institute.
6. (Jan 2014). "PDBsum additions". Nucleic Acids Research.
7. (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs". Nucleic Acids Research.