If You Use a Screen Reader

This content is available through Read Online (Free) program, which relies on page scans. Since scans are not currently available to screen readers, please contact JSTOR User Support for access. We'll provide a PDF copy for your screen reader.
Journal Article

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
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
Were these topics helpful?

Select the topics that are inaccurate.

  • Read Online (Free)
  • Subscribe ($19.50)
  • Add to My Lists
  • Cite this Item
Since scans are not currently available to screen readers, please contact JSTOR User Support for access. We'll provide a PDF copy for your screen reader.
Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome
Preview not available

Abstract

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.

Page Thumbnails

  • Thumbnail: Page 
5993
    5993
  • Thumbnail: Page 
5994
    5994
  • Thumbnail: Page 
5995
    5995
  • Thumbnail: Page 
5996
    5996
  • Thumbnail: Page 
5997
    5997
  • Thumbnail: Page 
5998
    5998