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PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank . It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of the interactions between them.
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PDBsum1 is a standalone version of PDBsum Generate for local installation and running. It generates the same analyses as PDBsum, with the added advantage of allowing you direct access to the computed data.
PDBsum1 tries to correct certain types of errors (eg missing chain identifiers, duplicate atom names, incorrect base names), but may not catch them all. If the programs fail to run correctly, you may need to check the file format.
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Many of the PDBsum1 analyses can be viewed in 3D using the RasMol molecular viewer. These include the structure as a whole, protein-ligand interasctions, and individual ProMotif motifs. PDBsum1 generates RasMol scripts to display these correctly. However, to view them needs a little set-up.
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PDBsum entry na. Go to PDB code: NONE PDB id
Sep 14, 2023 · You can upload your structure to PDBsum to have a full set of PDBsum analyses, including PROCHECK plots, generated for it. (Use the Generate option in the left-hand menu).
PDBe is a founding member of the Worldwide Protein Data Bank (wwPDB) which collects, organises and disseminates data on biological macromolecular structures. wwPDB Partners: RCSB PDB, PDBj, BMRB, EMDB. Read more about PDBe.
