Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive

By Stephen K. Burley, Helen M. Berman, Gerard J. Kleywegt, John L. Markley, Haruki Nakamura, S. Velankar. Methods in molecular biology, 2017

974 citations recorded by the source corpus.

The Protein Data Bank (PDB)—the single global repository of experimentally determined 3D structures of biological macromolecules and their complexes—was established in 1971, becoming the first open-access digital resource in the biological sciences. The PDB archive currently houses ~130,000 entries (May 2017). It is managed by the Worldwide Protein Data Bank organization (wwPDB; wwpdb.org), which includes the RCSB Protein Data Bank (RCSB PDB; rcsb.org), the Protein Data Bank Japan (PDBj; pdbj.org), the Protein Data Bank in Europe (PDBe; pdbe.org), and BioMagResBank (BMRB; www.bmrb.wisc.edu). The four wwPDB partners operate a unified global software system that enforces community-agreed data standards and supports data Deposition, Biocuration, and Validation of ~11,000 new PDB entries annually (deposit.wwpdb.org). The RCSB PDB currently acts as the archive keeper, ensuring disaster recovery of PDB data and coordinating weekly updates. wwPDB partners disseminate the same archival data from multiple FTP sites, while operating complementary websites that provide their own views of PDB data with selected value-added information and links to related data resources. At present, the PDB archives experimental data, associated metadata, and 3D-atomic level structural models derived from three well-established methods: crystallography, nuclear magnetic resonance spectroscopy (NMR), and electron microscopy (3DEM). wwPDB partners are working closely with experts in related experimental areas (small-angle scattering, chemical cross-linking/mass spectrometry, Forster energy resonance transfer or FRET, etc.) to establish a federation of data resources that will support sustainable archiving and validation of 3D structural models and experimental data derived from integrative or hybrid methods.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e2a94d0816680a688e3930efcae7f424a15eb9f3

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

Citations in the corpus

Mapping the Landscape of Artificial Intelligence Applications against COVID-19 (2020, background): “On the other hand, in terms of drug discovery, there are well-established initiatives such as the RCSB Protein Data Bank (Burley et al., 2017) and the Global Health Drug Discovery Institute Portal (GHDDI, 2020) † , which have created centralized portals with data and resources for better…”
Bringing diffuse X-ray scattering into focus (2017, background): “wwPDB [1], improvements in data processing pipelines, and the advent of completely unattended data collection,”
Protein language model embeddings for fast, accurate, alignment-free protein structure prediction (2021, methodology): “We obtained 77,864 high-resolution experimental three-dimensional (3D) structures from ProteinNet12 (AlQuraishi, 2019) compiled from the PDB (Burley et al., 2017) before the CASP12 submission deadline (Moult et al., 2018) thereby replicating the CASP12 conditions.”
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins (2017, background): “The new Mobi 2.0 software (42) is used to extract LIPs and disorder information from PDB files.”
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach (2017, methodology): “PDB, Protein Data Bank; APF, Atomic Property Field.”
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions (2020, background): “38 The original sources for each chemical record are cited with links to each database, allowing users to directly access the original data source for additional details.”