The Pairwise Structure Alignment Tool can align one or more protein chains to a reference structure in a pairwise manner.

This tool allows for simultaneous analysis and visualization of three-dimensional (3D) structure alignments and structure-based one-dimensional (1D) sequence alignments. The two panels displaying alignment results are interconnected and selecting residues in one panel will select and highlight the same residues in the other panel.

Access the Pairwise Structure Alignment Tool from the Analyze menu at the top of the page or directly from RCSB.org/alignment. User Guide Documentation is available, with examples of aligning PDB experimental structures with Computed Structure Models (CSMs) from AlphaFold and aligning PDB structures to related enzymes.

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The rcsb-api Python software package can be used for accessing RCSB.org Application Programming Interface (API) services. This package broadens access to RCSB.org features and data.
The package provides access to search and data API services, which are two of the main APIs that power RCSB.org.

Users can perform all the common types of Advanced Search queries on RCSB.org through a Pythonic interface. Users can also programmatically access and retrieve all metadata associated with 3D biostructures from RCSB.org via Python. Read more:

rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs
Dennis W. Piehl, Brinda Vallat, Ivana Truong, Habiba Morsy, Rusham Bhatt, Santiago Blaumann, Pratyoy Biswas, Yana Rose, Sebastian Bittrich, Jose M. Duarte, Joan Segura, Chunxiao Bi, Douglas Myers-Turnbull, Brian P. Hudson, Christine Zardecki, Stephen K. Burley
(2025) Journal of Molecular Biology 437: 168970
10.1016/j.jmb.2025.168970

MolViewSpec is a new Mol* extension to create molecular scenes that allows users to:

• Describe molecular scenes: what to load (structures, maps, annotations) and how to show it (representations, colours, labels, measurements, custom 3D shapes…). You can mix data types (structural, volumetric, annotations) in one scene with consistent styling.
• Share: to use the scenes, simply open the spec in Mol* in the browser or use the standalone Python package for scripted workflows.
• Reproduce: scenes make visuals reproducible across browsers, collaborators, and notebooks. No more “how did you make that figure?”.
• Automate figure creation and analysis by generating specs from Python pipelines.

Learn more and try examples at molstar.org. Read more:

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations
Adam Midlik, Sebastian Bittrich, Jennifer R Fleming, Sreenath Nair, Sameer Velankar, Stephen K Burley, Jasmine Y Young, Brinda Vallat, David Sehnal
(2025) Nucleic Acids Research 53: W408–W414
10.1093/nar/gkaf370

The Worldwide Protein Data Bank (wwPDB) partnership hosts the Protein Data Bank (PDB) archive of more than 240,000 experimentally determined 3D structures of biomolecules as part of the Registry of Open Data on Amazon Web Services (AWS). This arrangement allows RCSB PDB, US data center for the wwPDB, to leverage the AWS global infrastructure and services at no cost to the project nor data consumer.

AWS enables rapid data delivery of data files downloaded from RCSB.org (via files.rcsb.org). Cached access to data files is especially fast, by an order of magnitude faster than data served from local servers.

AWS is also used to serve annual snapshots of the PDB archive (in addition to snapshots hosted by PDBj (Japanese data center for the wwPDB). These snapshots provide readily identifiable data sets for research using the PDB archive.