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Photo of Mattias Ohlsson

Mattias Ohlsson

Professor

Photo of Mattias Ohlsson

Matching protein structures with fuzzy alignments

Author

  • R Blankenbecler
  • Mattias Ohlsson
  • Carsten Peterson
  • Markus Ringnér

Summary, in English

Unraveling functional and ancestral relationships between proteins as well as structure-prediction procedures require powerful protein-alignment methods. A structure-alignment method is presented where the problem is mapped onto a cost function containing both fuzzy (Potts) assignment variables and atomic coordinates. The cost function is minimized by using an iterative scheme, where at each step mean field theory methods at finite "temperatures" are used for determining fuzzy assignment variables followed by exact translation and rotation of atomic coordinates weighted by their corresponding fuzzy assignment variables. The approach performs very well when compared with other methods, requires modest central processing unit consumption, and is robust with respect to choice of iteration parameters for a wide range of proteins.

Department/s

  • Computational Biology and Biological Physics - Undergoing reorganization

Publishing year

2003-10-14

Language

English

Pages

11936-11940

Publication/Series

Proceedings of the National Academy of Sciences

Volume

100

Issue

21

Document type

Journal article

Publisher

National Academy of Sciences

Topic

  • Biophysics

Keywords

  • algorithm
  • mean field annealing
  • fuzzy assignment
  • dynamical programming

Status

Published

ISBN/ISSN/Other

  • ISSN: 1091-6490