De novo prediction of three-dimensional structures for major protein families

Richard Bonneau, Charlie E M Strauss, Carol A. Rohl, Dylan Chivian, Phillip Bradley, Lars Malmström, Tim Robertson, David Baker

Research output: Contribution to journalArticlepeer-review


We use the Rosetta de novo structure prediction method to produce three-dimensional structure models for all Pfam-A sequence families with average length under 150 residues and no link to any protein of known structure. To estimate the reliability of the predictions, the method was calibrated on 131 proteins of known structure. For approximately 60% of the proteins one of the top five models was correctly predicted for 50 or more residues, and for approximately 35%, the correct SCOP superfamily was identified in a structure-based search of the Protein Data Bank using one of the models. This performance is consistent with results from the fourth critical assessment of structure prediction (CASP4). Correct and incorrect predictions could be partially distinguished using a confidence function based on a combination of simulation convergence, protein length and the similarity of a given structure prediction to known protein structures. While the limited accuracy and reliability of the method precludes definitive conclusions, the Pfam models provide the only tertiary structure information available for the 12% of publicly available sequences represented by these large protein families.

Original languageEnglish (US)
Pages (from-to)65-78
Number of pages14
JournalJournal of Molecular Biology
Issue number1
StatePublished - 2002


  • Gene annotation
  • Pfam
  • Rosetta
  • Structural genomics
  • Structure prediction

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Molecular Biology


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