Protein Structure Prediction by Protein Threading

  • Ying Xu
  • Zhijie Liu
  • Liming Cai
  • Dong Xu
Chapter
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Abstract

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on “the inverse protein folding problem” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term “protein threading.” These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

Keywords

Energy Function Query Sequence Tree Decomposition Protein Structure Prediction Query Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Ying Xu
    • 1
  • Zhijie Liu
    • 2
  • Liming Cai
    • 3
  • Dong Xu
    • 4
  1. 1.Institute of Bioinformatics and Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthens
  2. 2.Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthens
  3. 3.Department of Computer ScienceUniversity of GeorgiaAthens
  4. 4.Computer Science DepartmentUniversity of Missouri-ColumbiaColumbia

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