Figure 2

Automatically seeded pages for each of the over 50,000 entries in the PDB. (a) The Proteopedia page '2ac0' [42] contains the structure of a protein-DNA complex showing the structural basis of DNA recognition by P53 tetramers [43]. (b) The Proteopedia page '2bbn' [44] shows an ensemble of 21 NMR (nuclear magnetic resonance) models for the solution structure of a calmodulin-target peptide complex [45]. Note how the ensemble of the 21 NMR models reveals the more flexible portions of the protein structure. These are two examples (a, b) of automatically seeded pages created for PDB entries. The title sentence, in bold, comes from the title in the PDB file, and the "Published Abstract from PubMed" section text comes from the abstract of the article associated with the structure (retrieved from PubMed). A rotatable/zoomable three-dimensional structure in Jmol is displayed, and, under it, useful information about the structure including green scene links highlighting functional sites and ligands (as available in the PDB file), plus a link for further visual exploration in FirstGlance in Jmol, and links to related genes, domains, related PDB entries, structural annotation (InterPro, Pfam, UniProt, SCOP, CATH), functional annotation (GO and GeneCards), links to other resources, and links to download the coordinates of the structure. The side-by-side placement of the abstract and the three-dimensional structure is of immediate value, and these seeded pages also serve as strong starting points for addition of content. The amount of information available on each PDB entry varies, and thus so do the lengths of seeded pages.