PDB Enhanced with New Query and Report 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 PDB production sites. These features include:
Ligand Search Capability. The SearchFields interface now provides a "Ligands and Prosthetic groups" field to enable queries for entries that contain a specific ligand. Ligands may be specified using either their common names or by the three-character identifiers found in the PDB HET group dictionary.
Expanded Information on Ligands and Prosthetic groups. The Structure Explorer interface now provides a table of ligands and prosthetic groups (referred to as "HET groups") within a particular macromolecule. While the previous interface only provided non-polymeric groups, the new implementation also shows non-canonical residues within protein or nucleic acid chains. A hyperlink provides convenient access to a graphical representation of these groups within Rasmol.
Direct Hyperlink to Primary Citation. Where available, hyperlinks to MEDLINE on the Structure Explorer summary page are now directly to the abstracts of the primary citations. The underlying information was collected and is maintained by the NIST data curation team within the RCSB. Note that the link to "Other Sources" within Structure Explorer holds an extensive set of links to all related publications within MEDLINE.
Faster and Improved Access to Dynamic Links. The static links previously available for each PDB entry from the Structure Explorer/Other Sources pages have been replaced by a dynamically updated and far more extensive set of links created by the Molecular Information Agent (MIA), developed by the NIH-funded National Biomedical Computation Resource at SDSC. Additional information on MIA is available from the PDB site. Access to the set of cross-links provided by MIA has been considerably improved after feedback generated from the initial deployment. All information is now broken down into categories and the initial screen only provides access to resources with direct links possible via the PDB identifier. Hyperlinks to extended sets of links allow convenient access to all other links.
Experimental Data Availability. Users can now limit queries to entries for which the experimental data were deposited. The SearchFields interface developed by the PDB-SDSC team now contains an "Experimental Data Availability" checkbox in the customizable section of the form. Checking this box and clicking the New Form button creates a form containing options for restricting the search to only those entries that were deposited along with experimental structure factors or NMR restraint files.
Expanded VRML Generation. The VRML interface for generating molecular images has been expanded to include options for scene annotation, for marking residues, drawing sites and symmetry copies. To access these features, select the option "VRML (custom options, full screen display)" from the View Structure page within Structure Explorer.
Cross-Linked Files for NMR-Determined Structures. The PDB now provides facile cross-linking of all files for NMR-determined structures. Coordinates sets for structures determined by NMR may be stored in several different PDB files with different PDB IDs, and the Structure Explorer page now provides cross-linking of these files. Specifically, if an averaged minimized structure is deposited to the PDB, this file is separate from the file or files containing the ensemble members comprising the multiple structure solutions.
In addition, new SearchFields queries for data collection information, number of chains and source organism have now been implemented in the beta test site. See the beta news page for more information.