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Structural Bioinformatics, 2nd Edition by Philip E. Bourne, Jenny Gu

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13

OTHER STRUCTURE-BASED DATABASES

J. Lynn Fink, Helge Weissig, and Philip E. Bourne

INTRODUCTION

The single repository for experimentally derived macromolecular structures is the Protein DataBank (PDB) (Bernstein et al., 1977; Berman et al., 2000; Berman et al., 2007) described in Chapter 11. The primary data provided by the PDB are the Cartesian coordinates, occupancies, and temperature factors for the atoms in these structures. Additional information given includes literature references, author names, experimental details, links to the sequence in the sequence databases, and some limited annotation of the biological function (Chapter 10). Collated into a single entry, due to the restrictions of the PDB format, or into multiple entries for very large X-ray structures and large NMR ensembles, these data constitute a concise description of the three-dimensional form of a molecule. The PDB currently releases the primary structure data once per week as requested by the depositor, whereupon a number of sites worldwide acquire these data via the Internet, derive additional information, and constitute a set of secondary resources. Secondary resources cover features such as stereochemical quality (Table 13.1), protein structure classification (Table 13.2), protein-protein interaction data (Table 13.3), structure visualization (Table 13.4), and data on specific protein families. The secondary resources described in this chapter can be viewed as downstream of the PDB in an information ...

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