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TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

D Kihara1, H Lu, A Kolinski

  • 1Laboratory of Computational Genomics, Donald Danforth Plant Science Center, 893 North Warson Road, St. Louis, MO 63141, USA.

Proceedings of the National Academy of Sciences of the United States of America
|August 16, 2001
PubMed
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A new computational method, TOUCHSTONE, aids in predicting protein structures from amino acid sequences. It uses threading-based restraints and a lattice model to accurately determine protein folding for genome-scale applications.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Folding

Background:

  • Accurate protein structure prediction from amino acid sequence is crucial.
  • Existing methods face challenges with efficient conformational search and accurate energy functions.

Purpose of the Study:

  • To develop and apply a novel ab initio protein folding methodology.
  • To improve the prediction accuracy of protein structures using threading-based restraints.

Main Methods:

  • Developed a threading-based method for secondary and tertiary restraint prediction.
  • Utilized a reduced lattice-based protein model with replica exchange Monte Carlo for conformational exploration.
  • Applied the TOUCHSTONE methodology to 65 proteins of varying lengths.

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Main Results:

  • Achieved root-mean-square deviation (RMSD) below 6.5 Å for 47 proteins and below 5 Å for 40 proteins within the five lowest energy centroids.
  • Prediction accuracy increased to 50 proteins upon incorporating atomic detail and a knowledge-based atomic potential.
  • Identified a reliable indicator for successful fold prediction: the ratio of relative contacts to protein length and the number of generated clusters.

Conclusions:

  • The TOUCHSTONE method demonstrates significant progress in ab initio protein structure prediction.
  • The identified indicator enables prediction of successful fold prediction likelihood.
  • This approach paves the way for genome-scale protein folding studies.