RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

By Stephen K. Burley, Helen M. Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, L. Costanzo, Cole H. Christie, K. Dalenberg, Jose M. Duarte, Shuchismita Dutta and 30 more. 2018

1,101 citations recorded by the source corpus.

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’

Subfields: Molecular Biology

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “Of the models deposited in the Protein Data Bank (PDB; Bernstein et al., 1977; Burley et al., 2019), 89% originate from X-ray crystallography.”
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, bioengineering and energy sciences (2020, background): “org since our last Nucleic Acids Research (NAR) Database Issue publication (10).”
Artificial intelligence to deep learning: machine intelligence approach for drug discovery (2021, background): “Further, the protein data bank (PDB) (https:// www. rcsb. org/) [62] is another freely accessible online repository that contains data of three-dimensional structures of proteins, DNA, RNA [63].”
PDBe: improved findability of macromolecular structure data in the PDB (2019, background): “org) (3), Protein Data Bank Japan (PDBj; pdbj.”
Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19 (2020, methodology): “The structure of SARS-CoV-2 protease (6LU7.pdb) available in Protein Data Bank (http://www.rcsb.org/) (Burley et al., 2019), was used as a receptor.”
RNA tertiary structure prediction using RNAComposer in CASP15 (2023, methodology): “40 We started the modeling process by running the 2D structure prediction programs operating within the RNAComposer system.”
AMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4 (2020, background): “A crystal structure of SAR405 in complex with human Vps34 is available in the Protein Data Bank [24] (PDB code: 4oys).”