In early July, the RCSB PDB released its newly reengineered beta site (pdbbeta.rcsb.org) for public testing. Some of the features of this site are described below.

Using PubMed Abstracts

Under an agreement with the National Library of Medicine (NLM; www.nlm.nih.gov), PubMed abstracts for the primary citation for structures are available on the beta site. For any given structure, the PubMed abstract can be accessed from the Structure Explorer Summary Page by clicking on the PubMed link under the Primary Citation. A web page is returned with the article title, abstract, keywords, authors, organizational affiliation, journal, and PubMed identifier. Clicking on the icon shown will launch a browser window containing the corresponding entry at PubMed (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed).

The text box at the bottom of this page can be used to search for structures in the PDB using any word in the abstract or keyword fields. Terms can be entered into the text box either by typing the word manually or by clicking the mouse over any word in the abstract or the keyword fields. This provides an alternative means to finding structures of interest.

Searching the PDB based on NMR Experimental Details

A new SearchFields feature is the ability to search for structures based upon specific NMR experimental parameters. These include NMR Experiment Type, Refinement Method, Selection Criteria, Spectrometer Manufacturer, Spectrometer Model, and Sample Conditions (for pH and Degrees Kelvin).

As with the current production site, searches may also be performed based upon experimental technique and the availability of constraint files.

Database Browsers

A major feature of the beta site is the ability to easily browse through database content based on the categories Biological Process, Cellular Component, Molecular Function, Enzyme Classification, Source Organism, Disease, Genome, SCOP Classification, CATH Classification, and Mutant Resource.

Each browser provides a hierarchical view of all the structures that are associated with the particular category or classification. Users can explore the category's hierarchy, view the number of associated PDB structures, and search for specific associated structures. The browsers are available from the left hand navigation bar and from the Search Fields menu items on the beta site. Detailed help and brow sing examples are available via the RoboHelp built into the reengineered site (in the left hand navigation bar, click on "Browse Database" and then on "How to Browse").

Any comments and suggestions about the browsers or any other beta site features may be sent to betafeedback@rcsb.org

WEBSITE STATISTICS

The RCSB PDB is available from several Web and FTP sites located around the world. Users are also invited to preview the newly reengineered RCSB web site at pdbbeta.rcsb.org/pdb.

The access statistics are given below for the primary RCSB PDB website at www.pdb.org.

DATA CD DISTRIBUTION

The last 2004 release of PDB data on CD-ROM has been distributed.

For 2005, the RCSB will distribute data to subscribers on DVD or CD-ROM each quarter.

The two-DVD quarterly sets will contain all structural and experimental data available in the archive at that time. The same data set on CD-ROM would currently require 20 disks.

The CD-ROM quarterly sets will contain structures released or modified during the previous three months.

Subscription ordering information is available here.