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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.
PDBsum is a comprehensive database of 3D structures in the Protein Data Bank, allowing users to browse, search and visualize protein molecules, interactions and functions.
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.
EMBL-EBI
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.
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.
Sep 14, 2023 · PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
PDBsum entry na. Go to PDB code:
EMBL's European Bioinformatics Institute: Big data for the life sciences.
Homepage | Protein Data Bank in Europe. 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.
