Large-scale determination of previously unsolved protein structures using evolutionary information

Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E. Kim, Hetunandan Kamisetty, Nick V. Grishin, David Baker

Research output: Contribution to journalArticle

114 Citations (Scopus)

Abstract

The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue–residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder.

Original languageEnglish (US)
Article numbere09248
JournaleLife
Volume4
Issue numberSeptember
DOIs
StatePublished - Sep 3 2015

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Proteins
Model structures
Set theory

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Medicine(all)
  • Neuroscience(all)

Cite this

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., ... Baker, D. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. eLife, 4(September), [e09248]. https://doi.org/10.7554/eLife.09248

Large-scale determination of previously unsolved protein structures using evolutionary information. / Ovchinnikov, Sergey; Kinch, Lisa; Park, Hahnbeom; Liao, Yuxing; Pei, Jimin; Kim, David E.; Kamisetty, Hetunandan; Grishin, Nick V.; Baker, David.

In: eLife, Vol. 4, No. September, e09248, 03.09.2015.

Research output: Contribution to journalArticle

Ovchinnikov, S, Kinch, L, Park, H, Liao, Y, Pei, J, Kim, DE, Kamisetty, H, Grishin, NV & Baker, D 2015, 'Large-scale determination of previously unsolved protein structures using evolutionary information', eLife, vol. 4, no. September, e09248. https://doi.org/10.7554/eLife.09248
Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE et al. Large-scale determination of previously unsolved protein structures using evolutionary information. eLife. 2015 Sep 3;4(September). e09248. https://doi.org/10.7554/eLife.09248
Ovchinnikov, Sergey ; Kinch, Lisa ; Park, Hahnbeom ; Liao, Yuxing ; Pei, Jimin ; Kim, David E. ; Kamisetty, Hetunandan ; Grishin, Nick V. ; Baker, David. / Large-scale determination of previously unsolved protein structures using evolutionary information. In: eLife. 2015 ; Vol. 4, No. September.
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