Data Exploration Services
2023 RCSB.org Statistics
Traffic is tracked using internally-developed tools.
| Month | Unique Visitors | Visits |
|---|---|---|
| January 2023 | 692,106 | 3,022,246 |
| February 2023 | 698,473 | 2,874,097 |
| March 2023 | 734,840 | 3,355,033 |
| April 2023 | 725,687 | 3,419,293 |
| May 2023 | 726,558 | 3,832,300 |
| June 2023 | 673,241 | 3,945,158 |
| July 2023 | 633,361 | 4,048,124 |
| August 2023 | 664,030 | 5,426,306 |
| September 2023 | 730,259 | 7,141,908 |
| October 2023 | 816,758 | 10,266,261 |
| November 2023 | 829,854 | 11,040,801 |
| December 2023 | 798,118 | 8,971,563 |
Explore Antibiotic Resistance in 3D
The Comprehensive Antibiotic Resistance Database (CARD) contains curated information about resistance genes, their products and associated phenotypes. Antibiotic resistance gene data classifications have been mapped to PDB sequences that are close homologs to sequences present in CARD.
RCSB.org can access these classifications using the Browse Annotations: CARD tool, through the Annotations Tab on Structure Summary pages (e.g., PDB ID 8EHH), and by searching by Antibiotic Resistance Ontology (ARO) numbers (e.g., ARO:3000001 for beta-lactamases)
Browse Annotations: CARD
This feature offers access to structures in the PDB archive by browsing different hierarchical trees. Related documentation is available.
Structure Summary Annotations Tab
Related structures will have CARD information included in the Annotations Tab. Related documentation is available.
Advanced Searching by Antibiotic Resistance Ontology (ARO)
Exact and close matches to the resistance genes were identified in PDB entries and annotated with relevant ARO identifiers and additional information antibiotics resistance related information. For example, you can search for all PDB sequences annotated as "determinant of antibiotic resistance" searching on (ARO:3000000).
New Features for Exploring Computed Structure Models at RCSB.org
RCSB.org offers access to >1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold (from ModelArchive).
Only experimentally-determined PDB structures are included in search results by default. Move the "Include CSM" from gray- to cyan-colored slider to activate.
New features have been added to help users explore access and study these models.
Download PAE JSON Files for AlphaFold Models
Predicted Aligned Error (PAE) files are an AlphaFold product of the AlphaFold system that helps to interpret the relative positions of domains in structure prediction. To assist users downloading AlphaFold CSMs via RCSB.org, a link has been added to download the PAE JSON file. Users can then read the PAE JSON file programmatically or through a visualization tool.
Structure Summary Page for a CSM from AlphaFold with the download PAE option highlighted by an arrow.
Access Computed Structure Model Annotations
Users can now explore Computed Structure Models (CSMs) and their connections to GO terms for Molecular Function, Cellular Component, and Biological Process (from Gene Ontology), protein family classification (InterPro), and disease associations (Pharos). The inclusion of these external annotations expands utility of studying CSMs at RCSB.org.
These annotations are accessible from the Structure Summary Annotations Tab for CSMs. For an example, see the Annotations Tab for the CSM of Alpha-enolase from AlphaFold.
Access Gene Ontology terms (for Molecular Function, Cellular Component, and Biological Process), InterPro protein family classifications, and Pharos disease associations for a CSM using the Annotation Tab.