The structural genomics experimental pipeline: Insights from global target lists

Nicholas O'Toole, Marek Grabowski, Zbyszek Otwinowski, Wladek Minor, Miroslaw Cygler

Research output: Contribution to journalArticle

33 Scopus citations

Abstract

Structural genomics (SG) initiatives are currently attempting to achieve the high-throughput determination of protein structures on a genome-wide scale. Here we analyze the SG target data that have been publicly released over a period of 16 months to assess the potential of the SG initiatives. We use statistical techniques most commonly applied in epidemiology to describe the dynamics of targets through the experimental SG pipeline. There is no clear bottleneck among the key stages of cloning, expression, purification and crystallization. An SG target will progress through each of these steps with a probability of approximately 45%. Around 80% of targets with diffraction data will yield a crystal structure, and 20% of targets with HSQC spectra will yield an NMR structure. We also find the overlaps among SG targets: 61% of SG protein sequences share at least 30% sequence identity with one or more other SG targets. There is no significant difference in average structure quality among SG structures and other structures in the PDB determined by " traditional" methods, but on average SG structures are deposited to the PDB twice as quickly after X-ray data collection.

Original languageEnglish (US)
Pages (from-to)201-210
Number of pages10
JournalProteins: Structure, Function and Genetics
Volume56
Issue number2
DOIs
StatePublished - Aug 1 2004

Keywords

  • NMR spectroscopy
  • Structural proteomics
  • X-ray diffraction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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