Prospects for ab initio protein structural genomics

TitleProspects for ab initio protein structural genomics
Publication TypeJournal Article
Year of Publication2001
AuthorsSimons, K. T., Strauss C., & Baker D.
JournalJournal of molecular biology
Date Published2001 Mar 9
KeywordsComputer Simulation, Computers, Databases as Topic, Genomics, Models, Molecular, Primary Publication, Protein Conformation, Protein Structure, Secondary, Proteins

We present the results of a large-scale testing of the ROSETTA method for ab initio protein structure prediction. Models were generated for two independently generated lists of small proteins (up to 150 amino acid residues), and the results were evaluated using traditional rmsd based measures and a novel measure based on the structure-based comparison of the models to the structures in the PDB using DALI. For 111 of 136 all alpha and alpha/beta proteins 50 to 150 residues in length, the method produced at least one model within 7 A rmsd of the native structure in 1000 attempts. For 60 of these proteins, the closest structure match in the PDB to at least one of the ten most frequently generated conformations was found to be structurally related (four standard deviations above background) to the native protein. These results suggest that ab initio structure prediction approaches may soon be useful for generating low resolution models and identifying distantly related proteins with similar structures and perhaps functions for these classes of proteins on the genome scale.

Alternate JournalJ. Mol. Biol.
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