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PDBsum


NAR Molecular Biology Database Collection entry number 278
Laskowski, R.A.
EMBL Outstation - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Contact roman@ebi.ac.uk

Database Description

PDBsum is a web-based atlas providing summary information and schematic diagrams for each macromolecular structural model deposited at the Protein Data Bank (PDB). It includes images of the structure, annotated plots of each protein chain's secondary structure, Pfam domains, detailed structural analyses generated by the PROMOTIF program, summary PROCHECK results, selected figures from the key reference, and schematic diagrams of protein-ligand. protein-protein and protein-DNA interactions. RasMol scripts highlight key aspects of the structure, such as the protein's domains, PROSITE patterns, and protein-ligand interactions, for interactive viewing in 3D. Numerous links take the user to related sites. PDBsum is updated whenever any new structures are released by the PDB. Additionally, users can upload their own strutural models, in PDB format, and get back a set of password-protected PDBsum analyses.

Acknowledgements

Major contributors include: Victor Chiskoff, Gail Hutchinson, Alex Michie, Andrew Wallace, Martin Jones, Andrew Martin, Nick Luscombe, Duncan Milburn, Atsushi Kasuya and Janet Thornton.

References

1. Laskowski R A (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res., 29, 221-222.
2. Laskowski R A, Hutchinson E G, Michie A D, Wallace A C, Jones M L, Thornton J M (1997) PDBsum: A Web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci., 22, 488-490.
3. Laskowski R A, Chistyakov V V, Thornton J M (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268.

Subcategory: Protein structure

Go to the abstract in the NAR 2014 Database Issue.
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