Abstract 1347 Training Opportunities: Exploring Experimental PDB Structures and Computed Structure Models from Artificial Intelligence/Machine Learning at RCSB Protein Data Bank (RCSB.org)

In addition to >210,000 atomic-level, experimentally-determined, three-dimensional (3D) structures of proteins and nucleic acids archived in the Protein Data Bank (PDB), the RCSB.org research-focused web portal of the RCSB Protein Data Bank (RCSB PDB) provides open access to >1 million Computed Structure Models (CSMs) generated using AlphaFold2 (from AlphaFold DB) and RoseTTAFold and AlphaFold2 (from the Model Archive). Both of these artificial intelligence/machine learning software tools were built on decades of methodological research in de novo protein structure prediction and depended critically on open access to the immense number of sequences in genomic sequence databases and the PDB archive. For the avoidance of doubt, experimentally-determined PDB structures and CSMs delivered on RCSB.org by the RCSB PDB are clearly identified as to their respective provenance and reliability. RCSB.org users can query, organize, visualize, analyze, and compare experimental PDB structures and CSMs side-by-side by utilizing powerful tools: Search: User queries can be applied to all PDB structures and CSMs; PDB structures only; and can exclude either PDB structures or CSMs from the search results. CSMs are not included in the search results by default. View and Organize Results: By default, search results are ordered using a query-based relevancy score. Results can be resorted using different criteria (e.g., listing experimental PDB structures first, per-residue confidence score (pLDDT)). Explore Similar Proteins: "Group" summary pages and search results simplify exploration of PDB structures with similar sequence identity/UniProt ID or were deposited as part of the same study. Explore Individual Structures: Structure Summary Pages offer details of experimental PDB structures and CSMs. Assess quality: Analogous to the validation slider for experimental structures, all CSMs report global and local confidence levels as pLDDT scores. Visualize in 3D: View experimental PDB structures and CSMs in Mol*. Use the standalone Mol* 3D Viewer to upload single or multiple data files, align structures, and run Structure Motif Search. Download: From Structure Summary Pages, download the ModelCIF data file hosted by the corresponding external archive. RCSB PDB will continue to develop resources to support exploration of experimentally-determined PDB structures alongside CSMs, scaling operations to accommodate growth in the PDB archive and increased availability of predicted structures. RCSB PDB offers a variety of resources to support graduate students, postdoctoral fellows, and researchers in CSM exploration, including virtual and in-person events, with related materials published at PDB-101 (PDB101.RCSB.org) and user guides and documentation published at RCSB.org. RCSB PDB Core Operations are funded by National Science Foundation (DBI-1832184), US Department of Energy (DE-SC0019749), and National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.