Section 24.5.3. The PDB database resource

In recognition of the fact that no single architecture can fully express the information content of the PDB, an integrated system of heterogeneous databases and indices that store and organize the structural data has been created. At present there are five major components (Fig. 24.5.3.1):

In the current implementation, communication among databases has been accomplished using the common gateway interface (CGI). An integrated web interface dispatches a query to the appropriate database(s), which then executes the query. Each database returns the PDB identifiers that satisfy the query, and the CGI program integrates the results. Complex queries are performed by repeating the process and having the interface program perform the appropriate Boolean operation(s) on the collection of query results. A variety of output options are then available for use with the final list of selected structures.

The CGI approach (and in the future a CORBA-based approach) will permit other databases to be integrated into this system, for example, those containing extended data on different protein families. The same approach could also be applied to include NMR data found in the BMRB or data found in other community databases.

Three distinct query interfaces are available for querying data within the PDB: Status Query (http://www.rcsb.org/pdb/status.html ), SearchLite (http://www.rcsb.org/pdb/searchlite.html ) and SearchFields (http://www.rcsb.org/pdb/cgi/queryForm.cgi ). Table 24.5.3.1 summarizes the current query and analysis capabilities of the PDB. Fig. 24.5.3.2 illustrates how the various query options are organized.

Table 24.5.3.1| top | pdf | Current query capabilities of the PDB (a) Query – single or iterative Free text – any word in the PDB Specific data items – compound name, author, description, deposition date, resolution, source, citation, cell dimensions, experimental method, data-collection method, refinement method, broad structure type, ligand (using the PDB HET records) Property pattern – sequence, secondary structure Structure similarity – 3D comparison (b) Results analysis – single structure Synopsis/Snapshot/Atlas – compound name, sequence, chemical components, citation, space group, cell constants, crystallization conditions, refinement details, structure views Quick report – compound name, author, description, deposition date, resolution, source, citation, cell dimensions, experimental method, data-collection method, refinement method, geometry features Full report – Quick report results plus secondary structure, chemical components, solvent Property profiles – sequence, secondary structure Links – see Table 24.5.3.2 Render – RasMol, Chime, QuickPDB (Java applet), VRML, Protein Explorer Geometry – bond lengths, bond angles, dihedrals, close contacts, summary visual inspection (c) Results analysis – multiple structure Quick report – as above, but collated over multiple structures Full report – as above, but collated over multiple structures Structure neighbours – pairwise structure comparison (d) Other query output options mmCIF and PDB data files Compressed files (gzip, tar, compressed)

Figure 24.5.3.2| top | pdf | The various query options that are available for the PDB.

SearchLite , which provides a single form field for keyword searches, was introduced in February 1999. All textual information within the PDB files as well as dates and some experimental data are accessible via simple or structured queries. SearchFields, accessible since May 1999, is a customizable query form that allows searching over many different data items, including compound, citation authors, sequence (via a FASTA search; Pearson & Lipman, 1988) and release or deposition dates.

Two user interfaces provide extensive information for results sets from SearchLite or SearchFields queries. The `Query result browser' interface allows access to some general information, access to more detailed information in tabular format and the possibility of downloading whole sets of data files for result sets consisting of multiple PDB entries. The `Structure explorer' interface provides information about individual structures as well as cross-links to many external resources for macromolecular structure data (Table 24.5.3.2). Both interfaces are accessible to other data resources through the simple CGI application programmer interface (API) described at http://www.rcsb.org/pdb/linking.html .

Table 24.5.3.2| top | pdf | Static cross-links to other data resources currently provided by the PDB Resource Information content 3Dee (Siddiqui & Barton, 1996) Structural domain definitions BMCD (Gilliland, 1988) Crystallization information about biomacromolecules CATH (Orengo et al., 1997) Protein fold classification CE (Shindyalov & Bourne, 1998) Complete PDB and representative structure comparison and alignments DSSP (Kabsch & Sander, 1983) Secondary-structure classification Enzyme Structures Database (Laskowski & Wallace, 1998) Enzyme classifications and nomenclature FSSP (Holm & Sander, 1998) Structurally similar families GRASS (Nayal et al., 1999) Graphical representation and analysis HSSP (Dodge et al., 1998) Homology-derived secondary structures Image (Sühnel, 1996) Image library of biological macromolecules MMDB (Hogue et al., 1996) Database of three-dimensional structures MEDLINE (National Library of Medicine, 1989) Direct access to MEDLINE at NCBI NDB (Berman et al., 1992) Database of three-dimensional nucleic acid structures PDBObs (Weissig et al., 1998) Obsolete structures database PDBSum (Laskowski et al., 1997) Summary information about protein structures SCOP (Murzin et al., 1995) Structure classifications STING (Neshich et al., 1998) Simultaneous display of structural and sequence information Tops (Westhead et al., 1998) Protein structure motif comparisons topological diagrams VAST (Gibrat et al., 1996) Vector Alignment Search Tool (NCBI) Whatcheck (Hooft et al., 1996) Protein structure checks

Table 24.5.3.3 indicates that usage has climbed dramatically since the system was first introduced in February 1999. Currently the PDB receives approximately 90 000 web hits per day, or, on average, one query every second, seven days a week, 24 hours a day.