Data Exploration Services

RCSB PDB APIs, RCSB.org, and PDB101.rcsb.org enforces the use of the secure HTTPS protocol. HTTP Strict Transport Security headers are implemented.

RCSB.org data and services have supported HTTPS protocol since 2017, but with this change all users will be redirected to HTTPS to guarantee secure communication.

Programmatic users are encouraged to switch to HTTPS as soon as possible. Not all HTTP clients will necessarily follow redirects automatically.

Individual website users should not be impacted, as modern web browsers will redirect automatically.

1S5L in Mol*

Membrane annotations from OPM, PDBTM, and MemProtMD have been integrated with PDB data.

A custom Mol* visualization enables prediction and visualization of the membrane layer placement.

Users access detailed information on the ‘Annotations’ tab of individual Structure Summary pages and browse OPM annotations using the ‘Browse Annotations’ feature.

Transmembrane sequence segments are highlighted in the 1D Protein Feature View.

Annotations in Protein Feature View

Documentation is available for these features.

New charts can be used to visualize the growth in the number of protein sequence clusters in PDB.

Number of Unique Protein Sequence Clusters within Released PDB Structures (Annual) shows the total number of unique protein sequence clusters in PDB by year.

PDB Statistics: Growth in Number of Protein Sequences in Released PDB Structures (Cumulative) shows the annual and cumulative numbers of protein sequences in released PDB structures.

These charts can be viewed at different levels of sequence identity.

A new paper describes the architectural redesign of RCSB PDB data delivery services that build on existing PDBx/mmCIF data schemas:

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley, John D. Westbrook

(2021) Journal of Molecular Biology 443: 166704 doi: 10.1016/j.jmb.2020.11.003

Documentation is available to help users learn the concepts and syntax behind the new web services described in the publication. Use this documentation to display all of the details of a specific API request, and then run the search request and to see the response.

3D Protein Feature View maps protein sequence features (annotations from RCSB PDB and external resources) on PDB structures.

• Navigate between 1D sequence features and 3D structure
• Select regions of interest
• Highlight interactions of specific residues
• Explore an environment of an ion/ligand

Help documentation is available.

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