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No. 7 - October 17, 2000

© 2000 RCSB

 

New Query and Reporting Features

The RCSB continues to enhance and upgrade the capabilities of the PDB customizable search interface and reporting output. Several new query and reporting features, previously available on the PDB beta test site, have been moved to the main PDB Web site and its mirrors. These features include:

Number of Chains and Source Organism
It is now possible to use the number of chains as derived from the PDB SEQRES as a search criteria via the SearchFields interface. To accomplish this, select the custom option "Number of Chains and Chain Length" and generate a new form to make this field available.

In order to query by source organism, select the custom option "Source" from the SearchFields interface and generate a new form. Specifications of the scientific name for source were parsed from the National Center for Biotechnology Information (NCBI)'s Macromolecular Database (MMDB) assignments. Users may also substitute a common name for a scientific name, such as a substitution of 'human' for 'Homo sapiens'. The curated data for source is currently available on the beta test site and will soon become available on the main PDB site and its mirrors.

Enzyme Classification
As previously described, a major development has been the accurate query of enzymes according to the Enzyme Commission classification. The combination of a complete enzyme classification of PDB structures, including the enzyme nomenclature, enables users to identify all structures available for a particular enzyme class at all four enzyme classification levels.

A convenient way of accessing all structures belonging to a particular enzyme class is provided with the EC Classification Browser linked to the SearchFields interface. To locate this information, simply choose the custom option "EC Number and Classification" and generate a new form.

The EC values are also available in the Structure Explorer pages.

Sequence Entries Cross-Link
Another addition to the PDB site concerns the Sequence Details available for every structure. The Sequence Details section of the Structure Explorer now points to the sequence entries in the major sequence databases corresponding to the particular structure being analyzed. This cross-link is currently limited to structures deposited after January 27, 1999.

Furthermore, the Structure Explorer interface has been enhanced with navigation arrows, for result sets larger than a single structure, that allow for browsing of individual structures within the set.