What's New in this Release (June 26, 2012)

 
Table of Contents:
 
  Query and Display Features
  Web Services
 
RCSB PDB Mobile
 
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The new RCSB PDB iPhone app provides fast, on-the-go access. Search the entire PDB, view the latest weekly release of structures, access your MyPDB account, view the entire catalog of Molecule of the Month articles, and more using either a WiFi or cellular data connection.

Click on the App Store link below to access the free download of RCSB PDB Mobile.
Further information is available on the app's information and FAQ pages. RCSB PDB Mobile is an update of the beta-tested PDBMobile.

A version of the app for the Android platform is in development.

 
 
 
 
 
New Author Profiles: Timeline Display of a Researcher's Structures
 
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Author Profiles are a new PDB-101 feature that display a vertical timeline of the structures that list a particular researcher as a Deposition Author or Primary Citation Author. To jump to a specific time period, select a year from the right navigation menu or scroll down the page to load subsequent years.

The structures shown are ordered by deposition date and can be sorted to display either the newest or the oldest structures first. Images are linked to the Structure Summary page for the entry.

The first instance of a protein or protein complex is displayed in larger font than subsequent examples of similar molecules.

 
 
 

To access this feature, select the link from the left hand RCSB PDB menu, or from the PDB-101 Features pull-down menu.
For individual profiles, type an author's last name into the search box of the Author Profiles page and click one of the available results. Author Profile URLs are permanent links that can be copied and shared.

For an example, visit J. Deisenhofer's Author Profile.

 
 
 
Query and Display Features
 

Advanced Search: All/Experimental Type/Molecule Type

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A new Advanced Search option can quickly access all PDB entries or a subset based on experimental and macromolecular type. At the same time, the "Remove Similar Sequences" checkbox can be used to refine the search.

For example, this feature can be used to easily retrieve all protein structures determined by X-ray crystallography or all PDB entries with 60% sequence similarity. Search results can be further refined, or used to generate reports.

 
 
 

Advanced Search: Structure Determination Method

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An Advanced Search option has been added to query entries based on structure determination method.

From the Advanced Search menu, scroll down to Methods, and select "Structure Determination Method." Select a text constraint from the pull-down menu (Equals/Contains/etc.) and enter the search text (e.g., molecular replacement, MAD, or SAD). Click "Submit Query" to execute the search, or "Results Count" to preview the number of entries that would be returned.

 
 
 

Structure Summary Feature: Revision History

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A new Structure Summary widget displays descriptions of the revision history of a PDB entry.

Since July 2011, the details of revisions made to a PDB entry have been publicly recorded in the mmCIF/PDBx file (in the category PDBX_VERSION). The Revision History widget lists these descriptions in the right hand column of the Structure Summary page. For an example, see the Structure Summary page for 1AJ5.

 
 
 

Query Feature: Other Search Suggestions

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To complement the options suggested by top bar searching, options for a Simple PDB Text Search and Other Search Suggestions have been added.

PDB textual information is organized in sections that require very different semantics. For example, a search for the word human (typically an attempt to find structures from the organism Homo sapiens) can also return structures deposited by an author named Human, J. The top bar autocomplete suggestions attempt to solve this problem by displaying the possible searches for each category.

For users who want a simple perform a simple, non-categorized text search, a link to perform a Simple PDB Text Search has been added.

The reverse is now also implemented in the search results. For cases where the text input is not found in any PDB entry, and it either matches associated ontology names (EC, GO etc.) or a specialized query format (a protein sequence string or a chemical SMILES string), Other Search Suggestions are displayed.

For example, performing a simple text search of the string "SVLATDISDESMTAAEENAASVA" will display a "No results" page that offers Other Search Suggestions with links to perform a sequence search (most likely the original intent).

 
 
 
 
Web Services
 

New Web Services to Access Domain-based Structural Alignments

In parallel with the domain-based structural alignments offered on the website, new Web Services provide access to information about precalculated 3D structure alignments. To request the representative domain for a chain of the Bacteriophage GA protein capsid 1gav:

To request all representative domains at 40% sequence identity: The names of the representative domains are either SCOP domain IDs (starting with "d") or domain IDs as have been assigned with the Protein Domain Parser software ("PDP:")

 
 
 

PubMedCentral ID

RESTful Web Services now also report PubMedCentral IDs. For example:

 
 
 

SOAP Service Retirement in 2013

SOAP services will be retired in 2013. Please migrate
your web services to corresponding RESTful services. Contact us with any questions