RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

AlphaFold Prediction of Structural Ensembles of Disordered Proteins

“…We based this approach on the observation that AlphaFold can predict inter-residue distances even for disordered proteins, despite having been trained on folded proteins. This is important because it enables the transfer of inter-residue distance information from folded proteins, whose accurate structures are available in large numbers in the Protein Data Bank (PDB) 19 for the training of deep learning methods, to disordered proteins, whose structural ensembles have been determined in much lower numbers and with less accuracy 20 .…”

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

“…The returning AlloMAPS database ( 25 ) now encompasses AFDB entries and other new-generation structure predictions, offering improved insights into the impact of mutations on allostery and helping design of allosteric drugs. The RCSB Protein Data Bank ( 26 ) reports that structure predictions, including AFDB, are now available via its website, alongside its core experimentally determined structures which now number almost 200 000. The update from GPCRdb ( 27 ) reports state-specific AF2 models alongside other new features such as lists of ligands for each receptor, both endogenous and surrogate.…”

A genomic and structural bioinformatic pipeline identifies candidate type VI secretion antibacterial effector-immunity pairs

“…T6EC1 had no known functional annotation based on its sequence, so we decided to use structural searches to understand its possible activity. We searched the Alphafold2 predicted structure of T6EC1 against PDB using Foldseek, a fast, structure based search algorithm 33,[63][64][65] . This revealed that T6EC1 has a striking structural similarity to Colicin M (PDB: 2XTQ) (Supplementary Figure 9).…”