After a period of testing at the PDB beta test site, select components of STING
Millennium Suite (SMS) are now available from the Structure Explorer pages of the
primary PDB Web site and its mirrors. SMS, a set of Java-based tools for the
simultaneous display of information about macromolecular structure and sequence,
was developed by Dr. Goran Neshich of Embrapa-CNPTIA (Campinas, Brazil) and
colleagues, in collaboration with Dr. Barry Honig's laboratory at Columbia University in
New York City, NY. The SMS links from the PDB site are served by an SMS mirror that
is being maintained at the San Diego Supercomputer Center.
The "Sequence Details" and "View Structure" sections of the Structure Explorer now
link to two interactive structure and sequence SMS views for any PDB structure, which
include options to access features such as a graphical display of amino acid contacts;
these views require Chime and a Java-enabled Web browser. A simpler "Protein Dossier"
view is also available from the "Sequence Details" section, offering a static graphical
summary of sequence- and structure-based properties, such as relative entropy and
The "Geometry" section of the Structure Explorer now links to a Ramachandran plot for
each PDB entry, also served from SMS, with options including the inter-connection of
data in a dihedral angle plot with the 3-D structure of the molecule. This view also requires
Java and Chime. SMS is also accessible from the "Other Sources" section of the Structure
Explorer for each PDB entry, under the category of Visualization resources.
Further information about this suite of tools is available from the SMS home page at
http://mirrors.rcsb.org/SMS/, and at http://www.rcsb.org/pdb/help-results.html. Comments may be sent to firstname.lastname@example.org.
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