Data Exploration Services
RCSB.org Statistics
RCSB.org is visited by millions of users each year. Traffic is tracked using internally-developed tools and filtered to remove robotic access.
| Month | Unique Visitors | Visits | Bandwidth |
|---|---|---|---|
| January 2022 | 607,078 | 3,052,321 | 22.8TB |
| February 2022 | 582,930 | 2,931,195 | 23.43TB |
| March 2022 | 666,545 | 3,191,671 | 28.98TB |
Explore Antibody Annotations
Use the Chemical Sketch Tool to draw or edit a molecule, then use the resulting SMILES or InChI string to search for matching molecular definitions in the PDB Chemical Component Dictionary.
This tool uses the web-based chemical drawing tool Marvin JS from ChemAxon to compose chemical sketches for chemical similar and substructure searches. Documentation is available.
The Chemical Sketch Tool can be acccessed from the top Search menu or from Advanced Search in the Chemical Search options (see image).
Select the Annotations Tab for an antibody to explore (PDB structure 6wps shown here).
Browse and Explore ECOD Annotations
ECOD (Evolutionary Classification of Protein Domains) annotations have been mapped to PDB structures.
The Evolutionary Classification Of protein Domains (ECOD) database classifies domains according to evolutionary relationships: (A) architecture, (X) possible homology, (H) homology, (T) topology, (F): Family.
Compared with other classification databases (e.g., SCOP, CATH) ECOD emphasizes distant evolutionary relationships.
These ECOD annotations have been mapped to PDB structures.
Explore ECOD classifications for a particular structure through the Annotations tab and the Sequence tab (Protein Feature View) for7ad1, a trimeric spike protein of SARS-CoV-2).
Use the ECOD Browser at RCSB.org to find proteins with a particular classification.
For more information on ECOD, see
ECOD: An evolutionary classification of protein domains
H. Cheng, R. D. Schaeffer, Y. Liao, L. N. Kinch, J. Pei, S. Shi, B. H. Kim, N. V. Grishin.
(2014) PLoS Comput Biol 10(12): e1003926 doi:10.1371/journal.pcbi.1003926
Search for Structures or Feature Help, News, and PDB-101
Use the pulldown menu to target queries of the PDB archive or Documentation
Users can now target searches towards PDB structures and related data or towards feature documentation, news, or PDB-101 content.
For PDB-focused searching, select "PDB Archive" from the pulldown option for the RCSB.org search box. This is set as the default.
To search for feature descriptions, news, and PDB-101 content, select the "Documentation" option.
MyPDB: Keep up-to-date with New Structures
The MyPDB service allows users to save any type of structure search (e.g., keyword, sequence, composite query).
Users can run these searches at any time, and receive email alerts when matching structures are released.
Documentation on how to save and run queries and alerts is available.
MyPDB can be accessed from either the turquoise MyPDB button at the upper right corner of any RCSB.org page, or from the "MyPDB" tab that appears with the Advanced Search Query Builder.
wwPDB News: Time-stamped Copies of PDB and EMDB Archives
A snapshot of the PDB Core Archive (ftp://ftp.wwpdb.org) as of January 3rd, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org.
A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 3, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.
The directory 20220103 includes the 185541 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 923 GB.
A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 3, 2022 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20220103/ and ftp://snapshots.pdbj.org/20220103/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (18059 and 254, respectively) and is 4.5 TB in size.
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