Protein Data Bank: the single global archive for 3D macromolecular structure data

By Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, L. Costanzo, Cole H. Christie, Jose M. Duarte, Shuchismita Dutta, Zukang Feng and 72 more. 2018

996 citations recorded by the source corpus.

Abstract The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.

Subfields: Materials Chemistry, Molecular Biology, Evaluation & Benchmarks, Computational Biology & Bioinformatics

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Citations in the corpus

Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, neutral): “The final structures were validated using the wwPDB validation tool 79,80 (https://validate-rcsb-east.wwpdb.org/ validservice/) and the Protein Structure Validation Suite (PSVS) 81 .”
Introducing “best single template” models as reference baseline for the Continuous Automated Model Evaluation (CAMEO) (2019, background): “are going to be published by the Protein Data Bank (PDB) 4 days later.(6) These structures serve as references for the evaluations”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, methodology): “Similar integration is done with SSEARCH (3) as part of services offered by the PDBe (11).”
PDBe-KB: collaboratively defining the biological context of structural data (2021, background): “For 50 years, the Protein Data Bank (PDB), managed by the worldwide Protein Data Bank consortium (wwPDB) (6), has served as the global archive for experimentally determined structures.”
Predicting protein flexibility with AlphaFold (2023, methodology): “The amino-acid sequences of these nine proteins were taken from their corresponding entries in the Protein Data Bank (PDB) (their PDB IDs are listed Table 1).”
CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods (2021, positive): “org) with the aim to shift the focus from the prediction of individual protein chains to the prediction of macromolecular complexes as determined experimentally by X-ray crystallography or increasingly cryo-EM techniques and deposited to the Protein Data Bank (PDB).(1) In this new CAMEO category, pa”
AlphaFill: enriching AlphaFold models with ligands and cofactors (2022, background): “Currently, we are transplanting 2,694 different compounds that represent over 95% of all ligand occurrences in the Protein Data Bank (PDB) 10 .”
Protein complex prediction with AlphaFold-Multimer (2021, methodology): “The Recent-PDB-Multimers set consists of all targets in the Protein Data Bank [13] released between 2018-04-30 and 2021-08-02.”