RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology,…

By Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, G. Crichlow, Cole H. Christie, K. Dalenberg, L. Costanzo, Jose M. Duarte and 28 more. 2020

1,313 citations recorded by the source corpus.

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction (2022, background): “PDBbind is a database curated based on the Protein Data Bank (PDB) [49].”
High-resolution de novo structure prediction from primary sequence (2022, methodology): “Algorithm 1: Protein language models based on the Gated Attention Module (GAU) Average Runtime (in seconds) more stable gradients especially at initialization ( 27–30 ).”
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 (2022, background): “org Documentation (see below) and other publications (47,48,110,115).”
Automated model building and protein identification in cryo-EM maps (2024, positive): “PDB files that included insertion codes, that is, additional residues relative to the reference sequence, were removed.”
Fast and accurate protein structure search with Foldseek (2022, methodology): “The AlpaFoldDB/UniProt50 (version 4), AlphaFoldDB/Proteome (version 4), AlphaFoldDB/Swiss-Prot (version 4), CATH50, ESM Atlas High-Quality Clu30 and PDB100 require 191 GB, 3.8 GB, 3.4 GB, 1.4 GB, 110 GB and 2.0 GB RAM, respectively.”
Single-sequence protein structure prediction using language models and deep learning (2022, background): “In addition to UniRef30, we used two other complementary databases (PDB70 and MGnify) to prepare a list of 77 proteins with the following properties: (1) they are at least 20 residues long; (2) they are orphans (that is, MSA depth = 1) across all three datasets simultaneously; and (3) they have solv”
Biasing AlphaFold2 to predict GPCRs and kinases with user-defined functional or structural properties (2022, background): “In fact, experimental protein structures represent only a small fraction of the complete set of known protein sequences (The Uniprot Consortium, 2019; Burley et al., 2021).”
UniProt: the Universal Protein Knowledgebase in 2023 (2022, background): “We continued the standardisation of all small molecule annotations in UniProtKB using the chemical ontology ChEBI (8), focusing on biologically relevant (or ‘cognate’) ligands such as activators, inhibitors, and cofactors and their corresponding binding sites, knowledge of which is captured from the”
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources (2022, background): “GPCRdb makes monthly updates of GPCR structures from the Protein Data Bank (PDB) (33) that are complemented with manual annotation of additional information about the receptors, endogenous ligands, bound ligands, bound transducer proteins, and auxiliary proteins.”
Cryo-EM targets in CASP14 (2021, neutral): “share is rising, with nearly 20% of structures submitted in 2021 coming from cryo-EM.(2) An adequate representation of cryo-EM structures in CASP is important for several reasons.”
Towards a structurally resolved human protein interaction network (2021, background): “The structural characterization of the human interactome has lagged behind, with experimental and homology models currently covering an estimated 15 protein interactions 4,5 .”