Rosetta in CAPRI rounds 13-19

Sarel J. Fleishman, Jacob E. Corn, Eva M. Strauch, Tim A. Whitehead, Ingemar Andre, James Thompson, James J. Havranek, Rhiju Das, Philip Bradley, David Baker

Research output: Contribution to journalArticle

  • 14 Citations

Abstract

Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13-19 we tested the ability of various backbone remodeling strategies to capture the main-chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large-scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement.

Original languageEnglish (US)
Pages (from-to)3212-3218
Number of pages7
JournalProteins: Structure, Function and Bioinformatics
Volume78
Issue number15
DOIs
StatePublished - Nov 15 2010
Externally publishedYes

Profile

Articular Range of Motion
RNA
Beta-Globulins
Dibenzoxepins
Eosinophil Chemotactic Factors

Keywords

  • Backrub
  • CAPRI
  • Conformational changes
  • Docking
  • Flexible-backbone modeling
  • Fragment insertion
  • Protein-protein interactions
  • RNA-protein interactions
  • Rosetta
  • Structure prediction

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Cite this

Fleishman, S. J., Corn, J. E., Strauch, E. M., Whitehead, T. A., Andre, I., Thompson, J., ... Baker, D. (2010). Rosetta in CAPRI rounds 13-19. Proteins: Structure, Function and Bioinformatics, 78(15), 3212-3218. DOI: 10.1002/prot.22784

Rosetta in CAPRI rounds 13-19. / Fleishman, Sarel J.; Corn, Jacob E.; Strauch, Eva M.; Whitehead, Tim A.; Andre, Ingemar; Thompson, James; Havranek, James J.; Das, Rhiju; Bradley, Philip; Baker, David.

In: Proteins: Structure, Function and Bioinformatics, Vol. 78, No. 15, 15.11.2010, p. 3212-3218.

Research output: Contribution to journalArticle

Fleishman, SJ, Corn, JE, Strauch, EM, Whitehead, TA, Andre, I, Thompson, J, Havranek, JJ, Das, R, Bradley, P & Baker, D 2010, 'Rosetta in CAPRI rounds 13-19' Proteins: Structure, Function and Bioinformatics, vol 78, no. 15, pp. 3212-3218. DOI: 10.1002/prot.22784
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J et al. Rosetta in CAPRI rounds 13-19. Proteins: Structure, Function and Bioinformatics. 2010 Nov 15;78(15):3212-3218. Available from, DOI: 10.1002/prot.22784

Fleishman, Sarel J.; Corn, Jacob E.; Strauch, Eva M.; Whitehead, Tim A.; Andre, Ingemar; Thompson, James; Havranek, James J.; Das, Rhiju; Bradley, Philip; Baker, David / Rosetta in CAPRI rounds 13-19.

In: Proteins: Structure, Function and Bioinformatics, Vol. 78, No. 15, 15.11.2010, p. 3212-3218.

Research output: Contribution to journalArticle

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