RCSB BETA SITE FEATURES
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
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
As with the current production site, searches may also be performed
based upon experimental technique and the availability of constraint
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 firstname.lastname@example.org
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
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