Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank
Fall 2011
Number 51
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Message from the RCSB PDB
Data Deposition
Deposition Statistics
Validate Structure Factor Diffraction Data with SF-Tool
New pdb_extract Release
wwPDB News
Data Query, Reporting and Access
Website Statistics
New Website Release
Different Ways To Explore New Entries
Outreach and Education
Tools for Education
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PDB40 Symposium
Education Corner
Christopher M. Smith, Ph.D., The Anatomy of Vision: Insights into Molecular Modeling for the Middle Schooler


Website Statistics

Access statistics for the second quarter of 2011 are shown.
Unique Visitorss
589.52 GB
642.00 GB
683.56 GB

New Website Release offers many new features for searching and browsing, including:

Quickly see how many entries are in a given category with the explore archive widgetExplore Archive widget: Tour the PDB archive by "drilling down" on significant properties of structures like Organism and Polymer type with just a few clicks using the home page's new Explore Archive widget. This widget provides a statistical overview of the PDB. Users can browse the charts individually, or view them all together by clicking on the "Show all" link. This widget applies the same drill-down options available from each set of search results to the contents of the entire archive.

Entering text in the All Categories top bar search returns search suggestions, organized by topic. Select any link to find all structures matching the query in that category.
Top search bar: The redesigned top search bar helps users easily and intuitively create both broad and precise searches. Start typing to access a suggestion box of related terms and links to searches. This box can be used to search a variety of categories, or limited to citation author, macromolecule name, sequence, or ligand. The order of results of a PDB text search or a sequence search is now based on the relevance of the term (for a text search) or the alignment score (for a sequence search).

Top of Structure Focus page for hemoglobin entry 1hho.
PDB-101 Structure Focus: Learn about the individual entries discussed in Molecule of the Month articles. Each Structure Focus page provides a description that explains why it was selected as an example structure, and offers an interactive 3D representation of the structure, sequence display, ligand information, and links to any other articles discussed in the Molecule of the Month feature. PDB-101 is a unique view of the RCSB PDB that packages together the resources of interest to teachers, students, and the general public.

PSI-MOD Protein Modification Browser is one of the ways users can browse through the PDB. To view all options, select the browse link from the top menu bar.
Search for structures by protein modification. The Protein Modification Browser was constructed based on protein modification ontology (PSI-MOD) from the Proteomics Standards Initiative ( From here, users can browse protein residue modifications, view the number of associated PDB entries, and search for associated structures. The related Advanced Search options have been expanded to include the protein modification source type (Name, Keyword, RESID, PSI-MOD, and Chemical Component Dictionary) and the associated name/ID of the modification. Check out the What's New page for complete descriptions of the newest RCSB PDB website features.

Different Ways To Explore New Entries

On average, 170 new entries are released into the PDB archive each week. The RCSB PDB offers different ways of exploring these new entries:

The Latest Structures widget, located on the home page, cycles through newly released entries..

The Latest Structures widget on the home page provides a slideshow of individual entries. It displays the entry title, image, citation, and a link to the PubMed abstract, if available. Users can pause the show at any point to read the entire abstract, click on the entry title to view the entry's Structure Summary page, or go straight to the Jmol view of the entry.

• The New Structures widget provides easy access to the Latest Structures added with the most recent weekly update. The structures will appear in the Query Result Browser, where users can drill through the structures by category (organism, taxonomy, experimental method, and more), generate reports, and download structure and sequences files.

The widget also links to a listing of the publications newly associated with PDB structures during the latest weekly update. This list includes links to the related PDB entry, the PubMed abstract, and related articles, and the unreleased entry search.

• The MyPDB service can be set to run saved searches with each update. Email alerts (weekly or monthly) will be sent when new entries matching the search are released in the PDB archive.

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