Data Exploration Services

RCSB.org Statistics: Q3

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Month Number of users Number of sessions
July 2024 463,460 1,096,807
August 2024 466,477 1,081,945
September 2024 548,875 1,233,829

Announcement: EDMAPS.rcsb.org Shutdown on October 16

The EDMAPS.rcsb.org service for mtz files will be retired on October 16, 2024 (see previous announcement). This service has been providing RCSB PDB-calculated electron density map coefficients for X-ray structures in the PDB archive. In June, this service stopped providing DSN6 formatted maps for these structures.

Electron density map coefficients will instead be provided by wwPDB for all X-ray structures in the PDB archive. These map coefficients will be the same as those used in wwPDB Validation Reports. All validation data will be available from the public archive at https://files.wwpdb.org/pub/pdb/validation_reports/.

Mol* at RCSB.org currently utilizes these electron density map coefficients in the Electron Density view.

Detailed support for this transition is available; additional questions can be sent to info@rcsb.org.

Deprecation of ligand model coordinates in MOL2/SDF format starting December 10

Decorative icon

Programmatic access should be updated to access model coordinates in CIF format

Starting December 10, 2024, RCSB PDB will no longer serve ligand model coordinates in MOL2 or SDF format. These files are currently served under https://files.rcsb.org/ligands/download/< ccd_id >_model.mol2 and https://files.rcsb.org/ligands/download/< ccd_id >_model.sdf.

Model and ideal coordinates for chemical components in CIF format will continue to be available from https://files.rcsb.org/ligands/download/< ccd_id >.cif.

Programmatic access should be updated as needed.

Ligand data files for ideal coordinates will continue to be served in MOL2 and SDF formats under

  • https://files.rcsb.org/ligands/download/< ccd_id >_ideal.mol2
  • https://files.rcsb.org/ligands/download/< ccd_id >_ideal.sdf

Information about all files available for download from RCSB PDB is available.

Paper Published: Exploring protein 3D similarities via comprehensive structural alignments

Structure Alignment Tool

Output of the pairwise alignment application.
 (2024) Bioinformatics 40: btae370 doi:10.1093/bioinformatics/btae370

This article introduces a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into RCSB.org. The tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith–Waterman 3D).

Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB.

This tool can also be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators.

By bridging the gap between 1D sequence and 3D structures of proteins, this tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses.

RCSB Protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Rose
(2024) Bioinformatics 40: btae370 doi:10.1093/bioinformatics/btae370