New and enhanced features have been added to the RCSB PDB, including:
See the What's New page for more new features and examples.
Protein Feature View for UniProt ID P69905 showing the new Exon Structure track
RCSB PDB's Protein Feature View visually summarizes how a full-length protein sequence from UniProt corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models 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 also displayed.
The Protein Feature View was recently redesigned to improve readability and to add descriptions of protein function, subunit structure, domains information, and genomic exon structure.
Protein Feature View can be launched from the "Molecular Description" section of a Structure Summary page (see 2d5z) as well as by searching for a UniProt ID (P69905) or Gene Symbol (Hba1). These Protein View images can be exported as Scalable Vector Graphics (SVG) files.
The PDB to UniProt mapping is based on the data provided by the SIFTS project.
Structure Summary pages for X-ray crystal structures provide access to validation information based upon the recommendations of the wwPDB X-ray Validation Task Force:
Previously, Ramachandran plots were located on the Structure Summary Geometry tab, which has been retired. Additional validation data and statistics are available from the Structure Summary Links tab, including reports by WHAT_CHECK and PROCHECK.
Ramachandran plots for entry 1cbs as created by MolProbity.
Set up a MyPDB account to create a personalized version of the RCSB PDB that is accessible from any computer.
Use the MyPDB widget in the left-hand menu to create an account and then log in to access stored setting and functionalities:
Saved Query Manager Features.
A) After saving a search to MyPDB, name it by clicking on the words "User Query" providing a more descriptive label.
B) The manager can be used to change email notification settings, run queries, and delete saved searches.
Use the Transporter Classification Browser to find PDB's membrane transport proteins as organized by TC Database family (www.tcdb.org). The browser will autocomplete search terms with the matching classifications, and highlight locations on the tree.
RCSB PDB's Browse Databasefeature offers access to structures in the PDB archive using different hierarchical trees.
Browsers are available to find structures organized around the following classifications:
Click Browse from the top of every RCSB PDB page and then the desired Browser Tab to start searching.
Month | Unique Visitors | Visits | Bandwidth |
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July 2014 | 218,350 | 599,228 | 1502.77 GB |
August 2014 | 216,099 | 512,845 | 1525.36 GB |
September 2014 | 292,187 | 673,001 | 2027.27 GB |