The young person's guide to the PDB

Wladek Minor, Zbigniew Dauter, Mariusz Jaskolski

Research output: Contribution to journalReview articlepeer-review

3 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)242-249
Number of pages8
JournalPostepy biochemii
Volume62
Issue number3
StatePublished - 1 Jan 2016
Externally publishedYes

Keywords

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

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