Message from RCSB PDB

In addition to nearly 200,000 experimentally-determined PDB structures, RCSB.org now offers access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold (from ModelArchive). Both software tools build on decades of methodological research on structure prediction and rely on open access to the immense number of sequences in genomic sequence databases and to the PDB archive. This release includes the pre-packaged collection of 999,255 AlphaFold models released on 01-Jun-2022 (based on model organism proteomes; global health proteomes; Swiss-Prot sequences; and MANE (Matched Annotation from NCBI and EMBL-EBI) and 1,106 protein complexes produced by RoseTTAFold and AlphaFold2 from the ModelArchive.

Only experimentally-determined PDB structures are included in search results by default. Move the "Include CSM" from gray- to cyan-colored slider to activate.

Exploring PDB Structures and CSMs at RCSB.org

Experimental structures and CSMs are clearly identified throughout the website: a dark-blue flask icon is used for PDB structures and a cyan computer icon for CSMs.

A confidence score called “predicted local distance difference test” (pLDDT) is computed for each amino acid residue to estimate how well the method has converged (i.e., how well the predicted structure agrees with multiple sequence alignment data and PDB structure information). This pLDDT score is used to color 2D and 3D views of CSMs and to sort search results.

RCSB.org users can query, organize, visualize, analyze, and compare experimental structures and CSMs side-by-side:

• 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. Turn the slider button to cyan to include CSMs when searching the tab bar Basic Search or Advanced Search options; 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)). The Refinements panel can be used to exclude PDB structures or CSMs from the results list.
• 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 (e.g., 4HHB) and CSMs (e.g., AF_AFP44795F1).
• 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* from Structure Summary Pages (e.g., AF_AFP44795F1). 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 (AlphaFoldDB or ModelArchive).

RCSB PDB will continue to develop resources to support exploration of experimental PDB structures and CSMs; feedback is greatly appreciated.

Learn about the protein structure-related tools, visualizations, and workflows that have been integrated into KBase on Thursday November 10, 2022 (1:00 - 5:00 pm EDT).

Registration is required for the Zoom meeting information, but attendance is at no charge. Please sign up at go.rutgers.edu/xfudv6m4.