Newsletter | Winter 2014 ⋅ Number 60

Data Query, Reporting, and Access

RCSB PDB's website was visited each month by an average of 320872 unique visitors and 737293 unique visits. A total of 19479 GB of data were accessed.

Month Unique Visitors Visits Bandwidth
January 2013 308327 703069 1785.92 GB
February 2013 317729 683177 1866.81 GB
March 2013 346548 765109 1529.32 GB
April 2013 369516 811545 1701.94 GB
May 2013 337920 765033 1669.93 GB
June 2013 291409 682857 1387.67 GB
July 2013 263698 655005 1392.55 GB
August 2013 259057 623656 1228.01 GB
September 2013 310025 733943 1505.25 GB
October 2013 383350 874037 1855.44 GB
November 2013 375120 864387 2000.50 GB
December 2013 287774 685699 1555.97 GB

Web Services provide remote access to RCSB PDB resources to help software developers build tools that efficiently interact with PDB data. The RESTful API offers:

  • Generic query options to execute any website search available as a Web Service call
  • Custom report services to return data in CSV, Excel, and XML formats
  • Specialized services to retrieve information about the status and description of PDB entries, chemical components, and sequence-based mappings
SOAP Web Services have been retired. Please contact us for any assistance with the transition to RESTful Web Services.

Drugs Bound to Primary Targets Table

Primary Drug Targets Table

Two new tables provide access to drug and drug target information from DrugBank that are mapped to PDB entries with each weekly update. These tables, accessed from the Tools menu, can be searched by generic or brand drug name, filtered, and sorted.

The Drugs Bound to Primary Targets Table lists drugs bound to primary target(s), or a homolog of primary target(s), i.e., co-crystal structures of drugs.

From this view, click on the tab for Primary Drug Targets to view related structures in the PDB, regardless if the drug molecule is part of the PDB entry (e.g., apo forms of drug targets, drug target with different bound ligands). Biotherapeutics, such as complexes with monoclonal antibodies, are included.

A detailed description of these Drug and Drug Target Mapping tables is online.

A gene name option is available from the simple search bar at the top of RCSB PDB pages. To begin, start typing the name of a gene (for example brca) and a list of possible suggestions will appear:

Then, select one of the suggestions in the "UniProt Gene Name" category. This will return a corresponding Protein Feature View page:

Among other things, the Protein Feature View page provides a graphical summary of a full-length protein sequence from UniProt and how it relates to PDB entries.

The PDB to UniProt mapping is based on the data provided by the Structure integration with function, taxonomy and sequence (SIFTS) initiative.

The Transporter Classification Database
( organizes membrane transport
proteins using the Transporter Classification (TC) system.
Similar to the Enzyme Commission (EC) system, it
incorporates both functional and phylogenetic information.

RCSB PDB's Browse Database option explores the PDB archive using different hierarchical trees. Each browser opens up to the top level in the hierarchy, and clicking on the arrow icons expands the respective nodes. A text box can also be used for related keyword searching. Clicking on the node's folder or name retrieves all PDB entries associated with the selected node.

Browsers are available to explore a variety of features, including GO Terms (for biological process, cell component, or molecular function), Enzyme Classification, Source Organism, Genome Location, Medical Subject Headings (MeSH), SCOP, CATH, ATC, Transporter Classification, and Protein Symmetry. Each browser can be selected from the corresponding tab.

This functionality is also an option in Advanced Search to combine these types of searches with queries for other specific types of data.

4HHB.A vs 4HHB.B using jCE click to launch

RCSB PDB's Comparison Tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, TM-Align, TopMatch, Dali).

Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) and circular permutations that are difficult for many alignment algorithms to detect (via jCE).

The Comparison Tool is also integrated with the Sequence Clusters offered from each entry's Sequence Similarity tab. Users can select a pair of chains from a given sequence cluster (with similarity cutoffs of 100%, 95%, 90%, 70%, 50%, 40%, or 30%) and run alignment comparisons.

Documentation and acknowledgements are available from the Compare Structures page.