Message from RCSB PDB

Search API v2 will be released April 13

Users should migrate to this new Search API. Please contact us with any questions.

Starting April 13, Version 2 of the RCSB PDB Search API will be available to better support access to RCSB PDB features. Version 1 Search APIs will remain operational, but not updated or corrected, for a limited period of time. On July 13, 2022, the V1 Search APIs will be removed and completely unresponsive.

Programmatic users are encouraged to use a preview server at search-beta.rcsb.org to review any code changes needed before v2 is released.

Documentation is available to help developers migrate from v1 to v2.

Switch to New Sequence Cluster Files by April 12

Sequence clustering based on polymer entity ID are now available to replace files organized by chain identifiers.

RCSB.org has introduced new files that contain the results of the weekly clustering of protein sequences in the PDB by MMseqs2 at 30%, 40%, 50%, 70%, 90%, 95%, and 100% sequence identity. Note that these files use polymer entity identifiers, instead of chain identifiers to avoid redundancy. The files are plain text with one cluster per line, sorted from largest cluster to smallest.

Files containing chain-based clustering will be updated only until April 12, 2022. Users should migrate to the new entity-based files as soon as possible.

This change enables more efficient delivery of sequence clustering data.

The latest issue of Protein Science offers A Compilation of Tools for Protein Science and includes

PDB-101: Educational resources supporting molecular explorations through biology and medicine (2022) Protein Science 31: 129-140 doi:10.1002/pro.4200

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D (2022) Protein Science 31: 187-208 doi:10.1002/pro.4213

The latest issue of Structure has a Focus on structural tools in biological discovery that includes

RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens
(2022) Structure 30: P55-68.e2 doi:10.1016/j.str.2021.10.008

In this article, David S. Goodsell and Stephen K. Burley examine the structural biology underpinning the success of SARS-CoV-2 mRNA vaccines and present freely available resources at the RCSB Protein Data Bank that could guide the structure-facilitated design of new countermeasures against existing and emerging viral pathogens.

Other new journal articles include

Simplified quality assessment for small-molecule ligands in the Protein Data Bank
 (2022) Structure 30: 252-262.e4 doi:10.1016/j.str.2021.10.003

RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
(2022) Bioinformatics 38: 1452-1454 doi:10.1093/bioinformatics/btab813

RCSB PDB also published the 2021 Annual Report (PDF) to provide an overview of recent Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education activities.

This report also looks back at the year-long celebration of 50 years of the PDB archive.

Download the 2021 Annual Report PDF

CASP (Critical Assessment of protein Structure Prediction) is in search for targets for the upcoming CASP15 modeling experiment (starting in May 2022). CASP community experiments aim to advance the state of the art in protein structure modeling. Every other year since 1994, CASP collects information on soon-to-be released experimental structures, passes on sequence data to the structure modeling community, and collects blind predictions of structure for assessment. Typically, about 100 modeling groups from around the world participate. Results of CASP experiments are assessed by leaders in the field (Independent Assessors), and published in special issues of the journal PROTEINS.

Visit the rcsb.org to learn more.