» Articles » PMID: 32695409

The Data Universe of Structural Biology

Overview
Journal IUCrJ
Date 2020 Jul 23
PMID 32695409
Citations 11
Authors
Affiliations
Soon will be listed here.
Abstract

The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.

Citing Articles

Metal ions in biomedically relevant macromolecular structures.

Majorek K, Gucwa M, Murzyn K, Minor W Front Chem. 2024; 12:1426211.

PMID: 39246722 PMC: 11378719. DOI: 10.3389/fchem.2024.1426211.


Building a FAIR image data ecosystem for microscopy communities.

Kemmer I, Keppler A, Serrano-Solano B, Rybina A, Ozdemir B, Bischof J Histochem Cell Biol. 2023; 160(3):199-209.

PMID: 37341795 PMC: 10492678. DOI: 10.1007/s00418-023-02203-7.


Common measures in mental health: a joint initiative by funders and journals.

Farber G, Gage S, Kemmer D, White R Lancet Psychiatry. 2023; 10(6):465-470.

PMID: 37084745 PMC: 10198931. DOI: 10.1016/S2215-0366(23)00139-6.


Exploring Scoring Function Space: Developing Computational Models for Drug Discovery.

Bitencourt-Ferreira G, Villarreal M, Quiroga R, Biziukova N, Poroikov V, Tarasova O Curr Med Chem. 2023; 31(17):2361-2377.

PMID: 36944627 DOI: 10.2174/0929867330666230321103731.


2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data.

Trewhella J, Jeffries C, Whitten A Acta Crystallogr D Struct Biol. 2023; 79(Pt 2):122-132.

PMID: 36762858 PMC: 9912924. DOI: 10.1107/S2059798322012141.


References
1.
Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

2.
Zhu X, Turner H, Lang S, McBride R, Bangaru S, Gilchuk I . Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies. Cell Host Microbe. 2019; 26(6):729-738.e4. PMC: 6908751. DOI: 10.1016/j.chom.2019.10.002. View

3.
Ulrich E, Markley J, Kyogoku Y . Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq Data Anal. 1989; 2(1):23-37. View

4.
Lawson C, Baker M, Best C, Bi C, Dougherty M, Feng P . EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 2010; 39(Database issue):D456-64. PMC: 3013769. DOI: 10.1093/nar/gkq880. View

5.
Masson G, Burke J, Ahn N, Anand G, Borchers C, Brier S . Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. 2019; 16(7):595-602. PMC: 6614034. DOI: 10.1038/s41592-019-0459-y. View