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Prospects for ab initio protein structural genomics
| Venue: | J Mol Biol |
| Citations: | 72 - 11 self |
BibTeX
@ARTICLE{Simons_prospectsfor,
author = {Kim T. Simons and Charlie Strauss and David Baker},
title = {Prospects for ab initio protein structural genomics},
journal = {J Mol Biol},
year = {}
}
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Abstract
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 a and a/b proteins 50 to 150 residues in length, the method produced at least one model within 7 AÊ 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.
Keyphrases
ab initio protein structural genomics native protein large-scale testing ab initio protein structure prediction native structure structure match amino acid residue structure-based comparison low resolution model genome scale novel measure ab initio structure prediction approach rosetta method standard deviation similar structure small protein traditional rmsd
