The prediction of the structures of proteins without detectablesequence similarity to any protein of known structure remains anoutstanding scientific challenge. Here we describe de novo blindstructure predictions of unprecedented accuracy for two proteins in large families made 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 use the method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three dimensionalstructures 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.
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