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Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome
Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick
Proceedings of the National Academy of Sciences of the United States of America
Vol. 99, No. 9 (Apr. 30, 2002), pp. 5993-5998
Published by: National Academy of Sciences
Stable URL: https://www.jstor.org/stable/3058613
Page Count: 6
You can always find the topics here!Topics: Proteins, Centroids, Genomes, Energy, Databases, Z score, Nucleic acids, Prospecting, Topology
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An ab initio protein structure prediction procedure, TOUCHSTONE, was applied to all 85 small proteins of the Mycoplasma genitalium genome. TOUCHSTONE is based on a Monte Carlo refinement of a lattice model of proteins, which uses threading-based tertiary restraints. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Selection of the native fold was done by using the convergence of the simulation from two different conformational search schemes and the lowest energy structure by a knowledge-based atomic-detailed potential. Among the 85 proteins, for 34 proteins with significant threading hits, the template structures were reasonably well reproduced. Of the remaining 51 proteins, 29 proteins converged to five or fewer clusters. In the test set, 84.8% of the proteins that converged to five or fewer clusters had a correct fold among the clusters. If this statistic is simply applied, 24 proteins (84.8% of the 29 proteins) may have correct folds. Thus, the topology of a total of 58 proteins probably has been correctly predicted. Based on these results, ab initio protein structure prediction is becoming a practical approach.
Proceedings of the National Academy of Sciences of the United States of America © 2002 National Academy of Sciences