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Threading algorithms

Part 4. Bioinformatics

4.8. Modern Programming Paradigms in Biology

Specialist Review

  1. Jadwiga Bienkowska1,2,
  2. Rick Lathrop3

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g409202

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Bienkowska, J. and Lathrop, R. 2005. Threading algorithms. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.8:99.

Author Information

  1. 1

    Serono Reproductive Biology Institute, Rockland, MA, USA

  2. 2

    Boston University, Boston, MA, USA

  3. 3

    University of California, Irvine, CA, USA

Publication History

  1. Published Online: 15 APR 2005

Abstract

This chapter reviews various algorithms that have been developed for protein structure prediction by threading. Threading algorithms depend on many features of protein sequence and structure representations and not all of them are used by all methods. There is no standard formalism to represent those different features. While providing necessary detail, sometimes the formal notation obscures the core idea of an algorithm. In order to make the core ideas transparent to many readers, we made an effort to adhere to a simple formalism and tried to avoid mathematical formulas. This forced us to omit many details and complete outlines of algorithms, for which the reader is referred to the original literature for a detailed picture.

Keywords:

  • structure prediction;
  • inverse folding;
  • threading;
  • sequence similarity;
  • structure similarity;
  • algorithms