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What's New in this Release (October 23, 2012)

 
Table of Contents:
 
  Improved Macromolecule Name Search
  Drug Name Search and Drug Annotations
  Four Synchronized Views to Browse Search Results
  Miscellaneous
 
Mapping PDB Structures to Full-length Protein Sequences
 

The Protein Feature View provides a graphical summary of a full-length protein sequence from UniProt and how it corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models information from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder (computed with JRONN) and hydrophobic regions (as computed using a sliding window approach) are displayed.

By default, representative PDB entries are used to give an overview for which regions of the UniProtKB sequence PDB entries are available. This view can be expanded to show all available PDB entries

This feature is available from the Molecular Description widget on Structure Summary pages. Selecting the Protein Feature View link launches more display options.

View an example Protein Feature View.

 
 
 
 
 
Improved Macromolecule Name Search
 

Improved Handling of Viral Polyproteins and Other Multi-component Proteins

To enable more accurate search results, polyproteins and multi-component proteins are now cross-referenced with PDB entities (MOL_IDs) at the component level based on alignment and residue ranges from UniProt.

For example, type "Gag-Pol" in the top bar search to see suggestions to retrieve all Gag-Pol polyprotein structures or only those for a particular component (protease, reverse transcriptase, integrase, etc.)

Another example are caspases, which are expressed as zymogens, that are proteolytically cleaved into two subunits. Type "Caspase" in the top search bar. The search suggestions list the subunits, for example: Caspase-1 subunit p20, Capspase-1 subunit p10.

 
 
 

PDB Entity Names as Synonyms for Macromolecule Names

Macromolecule name searches in the top menu bar make suggestions based on UniProt names. To provide more accurate suggestions, frequently used names of PDB entities have been assigned as synonyms for the corresponding UniProt names.

For example, by typing HIV-1 protease on the top bar search, users are provided with a suggestion to retrieve all "HIV-1 protease (Gag-Pol polyprotein, Protease)" structures for HIV-1 organisms.

Using synonyms makes the suggestions list more powerful than plain text searching. It makes PDB entries that use alternative molecule names such as retropepsin easier to find.

 
 
 

Short Name Search

The top bar molecule name search also provides suggestions for alternative and short synonyms from UniProt.

For example typing "cam" suggests retrieving all CaM (Calmodulin) structures.

 
 
 
 
 
Integration with DrugBank: Drug Name Searches and Drug Annotations
 

Drug Name Autocomplete

Drug and drug target data from DrugBank (http://www.drugbank.ca) have been integrated with the RCSB PDB website. The top bar search supports auto-complete for generic and brand names of drugs.

DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41. DOI: 10.1093/nar/gkq1126

 
 
 

Drug Info on Ligand Summary Page

A Drug Info widget on the Ligand Summary pages lists the corresponding data from DrugBank (when available). The widget contains DrugBank ID, drug name, groups, brand name, and more, with links to the corresponding data at DrugBank.

Show Ligand Summary page for Lipitor (ligand ID: 117)

 
 
 
 
Four Synchronized Views to Browse Search Results
 

To help users browse search results, new options have been added. In addition to the original results browser, now called the "detailed view," we have added a consensed view, a new gallery view, and a timeline view. The views are synchronized; selecting or deselecting a structure in one view will have the same effect in the others.

Condensed

The condensed view concisely lists structures, showing only the PDB ID, title, and macromolecule name found in their results.

 
 
 

The gallery view shows only the structure image and PDB ID. Images can be resized by using the options dropdown. The PDB ID links to the Structure Summary page for the entry.

 
 
 

Timeline

The timeline view takes the current search results and generates a visual timeline ordered by release date, similar to the Author Profile feature.

The PDB IDs shown in the timeline link to their respective Structure Summary pages. To avoid performance issues, search results that return more then 3000 results have their timeline view disabled. A future release will re-enable this feature for all search queries.

 
 
 
 
Miscellaneous
 

PSI and PSI:Biology Structures

Structure Summary pages now display the related logos for structures from the PSI:Protein Structure Initiative and PSI:Biology projects.

 
 
 

Tabular Reports (PubMedCentral ID)

PubMed Central IDs are now included in the "Primary Citation" and customized tabular reports. Each PubMed Central ID is hyperlinked to the corresponding article at PubMed Central.

The Tabular Report system provides a broad view of PDB data and a friendly interface for users to browse, filter, and search the data. Users can view data in various predefined standard reports or by creating customized reports with selected data items. For more details please refer to the Tabular Report help page.

 
 
 

Searching by Pfam Accession Number

Entering a Pfam Accession Number, Pfam Family Identifier, or Pfam Description in the top search box will identify all PDB entries related to that specific Pfam domain.

 
 
 

Pairwise Structural Alignments with Dali

Dali pairwise structural alignments have been added to the Compare Structures tool. Dali computes optimal and suboptimal structural alignments between two protein structures.

Advances and pitfalls of protein structural alignment. Hasegawa H, Holm L (2009) Curr. Opin. Struct. Biol. 19, 341-348. DOI: 10.1016/j.sbi.2009.04.003

 
 
 

An external link to AtlasCBS has been added to the Structure Summary page's Link tab under the Ligand Features section. View external links tab for 1A4G

Given a target-ligand database with chemical ligand structures and associated biological affinities/activities, the AtlasCBS server generates two-dimensional, dynamical, representations of its content based on ligand efficiency indices. These variables allow an effective decoupling of the chemical (angular) and biological (radial) components. BindingDB, PDBBind and ChEMBL databases are currently implemented. Proprietary datasets can also be uploaded and compared.

AtlasCBS: a web server to map and explore chemico-biological space. See Álvaro Cortés-Cabrera, Antonio Morreale, Federico Gago and Celerino Abad-Zapatero (2012) J. Computer-Aided Molecular Design, DOI: 10.1007/s10822-012-9587-5.