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Postepy Biochem. 2016;62(3):242-249.

The young person's guide to the PDB.

Author information

1
University of Virginia, Charlottesville, VA 22908, USA.
2
Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.
3
Zakład Krystalografii, Wydział Chemii, Uniwersytet im. A. Mickiewicza w Poznaniu ul. Grunwaldzka 6, 60-780 Poznań, Polska.
4
Centrum Badań Biokrystalograficznych, Instytut Chemii Bioorganicznej PAN, ul. Z. Noskowskiego 12/14, 61-704 Poznań, Polska.

Abstract

in English, Polish

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

KEYWORDS:

Protein Data Bank; data mining; macromolecular structure; structural biology; structural databases; structure validation

PMID:
28132477
PMCID:
PMC5610703
[Indexed for MEDLINE]
Free PMC Article

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