The December 17, 2013 release offers:
Membrane Protein Annotation
Ligand & Crystal Packing Visualization
Improved Tabular Reports
SOAP Retirement and Miscellaneous
Membrane Proteins Annotation
Search for Membrane Proteins in the PDB
Membrane proteins in the PDB have been identified and annotated using either:
- Membrane proteins of known 3D Structure, mpstruc database developed by the Stephen White lab at UC Irvine.
- Inferred by homology (structures with sequences that are at least 90% identical to those annotated by mpstruc).
Example drilling down through the Membrane protein data distribution.
Membrane Protein Drill Down. Membrane proteins are classified by mpstruc using a 3-level hierarchy
- Major function
- Specific function
Specific classes of Membrane proteins can be easily accessed from the 'Explore Structure' widget on the home page or the 'Drill-down' option to refine query results.
Browse Database option for Membrane proteins
Membrane Protein Browser. The Membrane Protein Browser also allows navigation of the 3-level hierarchy as well as text search with autocomplete. At each level of the hierarchy the number of structures is displayed.
Membrane annotation on Search Results
Membrane annotation on a Structure Summary page
Membrane Protein Annotation. The query results and structure summary pages display Membrane protein annotation.
3D Visualization (Jmol) Features
Ligand Binding & Crystal Packing
Options for visualizing binding sites and crystal packing have been added to the Jmol features offered.
We thank Robert Hanson (St. Olaf College), the current principal Jmol developer, for implementing these features during his recent visit to the RCSB PDB.
Binding Site Visualization. Select the Ligand tab at the bottom of the Jmol view to access a new feature that displays residues in contact with a selected ligand. A cropped ligand van der Waals surface is color coded by the proximity to the van der Waals surface of the binding site (red: close contact, blue: far contact).
View Biotin binding site in PDB entry 1STP. Scroll to the bottom of the '3D View' page to access the Ligand tab.
Crystal Packing Visualization. Options for unit cell display and crystal packing have been improved for the asymmetric unit view. Neighboring unit cells can be displayed in one dimension (3x1) or in two dimensions as a (3x3) grid along the unit cell vectors.
3D Ligand View. A 3D ligand view has been added to Ligand Summary page.
Improved Tabular Reporting
Clear & Simple to Use
Drug & Drug Target Mapping Tables. The tables (view) can be exported as an Excel spreadsheet (.xls, .xlsx) or comma separated value (.csv) file.
Fixed Index Column. The PDB ID column in a tabular report will now remain displayed as the scroll-bar is moved to the right to view additional columns (see example below).
Custom Report RESTful Web Service for Entire Archive. The custom tabular report RESTful Web Service has been extended to suppport large tables. By specifying 'pdbids=*' in the URL, a table of all PDB entries can be generated. Since these reports are large, the comma separated value format (.csv) is recommended. For example the following URL retrieves a custom report for all current PDB entries and the selected columns (structure id, structure title, experimental technique) in .csv format:
More information is available about Custom Report Web Services.
SOAP Retirement, Advanced Search
SOAP services have been retired with this software release as announced previously.
Please migrate any remaining SOAP service calls to our RESTful Web Services.
The RESTful API offers:
- Generic query to execute any search available on the website as a Web Service call.
- Custom report service which offers a flexible way to return data in CSV, Excel, and XML format.
- Specialized services to retrieve information about the status and description of PDB entries, chemical components, and sequence-based mappings.
Please contact us for any assistance with the transition from SOAP to RESTful.
PubMed ID Search. A PubMed ID field has been added to the Citation Advanced Search. By unchecking the 'Primary citation only' checkbox, secondary citations can also be searched by PubMed ID.
Protein Symmetry Advanced Search. Protein Symmetry Advanced Search now uses a pull-down menu to select the symmetry and a range search for RMSD (min, max value) has been added. The RMSD is the Cα RMSD for related subunits in the biological unit and is a measure of the overall symmetry. For pure crystallographic symmetry, the RMSD is 0, whereas for non-crystallographic symmetry the RMSD is between > 0 and ≤ 7 Å.