RCSB Protein Data Bank: Tools for Analysis and Visualization of Biological Macromolecules

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Abstract
Through the RCSB.org research-focused web portal, many millions of users access rigorously validated, expertly biocurated, 3D biostructure information stored in the Protein Data Bank (PDB) archive alongside predicted Computed Structure Models (CSMs) from AlphaFold DB and ModelArchive. Specialized tools and related resources, from 3D visualization to protein annotations, allow deep exploration of this rich trove of data. The recently updated RCSB.org Advanced Search interface provides a more intuitive experience with enhanced support for 3D structure exploration. The 3D Similarity Search option is powered by a new AI-based system that is more accurate and scalable to much larger collections of structures. Additional capabilities are provided through web-based APIs and a Python API wrapper package that enable researchers to easily interact with RCSB PDB programmatic services for individually tailored analyses. These resources, together with a statistics tool, training and documentation, and the upcoming wwPDB ID and archive transition, are described.