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Matching protein structures with fuzzy alignments

Författare:
  • R Blankenbecler
  • Mattias Ohlsson
  • Carsten Peterson
  • Markus Ringnér
Publiceringsår: 2003
Språk: Engelska
Sidor: 11936-11940
Publikation/Tidskrift/Serie: Proceedings of the National Academy of Sciences
Volym: 100
Nummer: 21
Dokumenttyp: Artikel i tidskrift
Förlag: National Acad Sciences

Abstract 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.

Keywords

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

Other

Published
  • ISSN: 1091-6490
Markus Ringnér
E-post: markus [dot] ringner [at] biol [dot] lu [dot] se

Forskningsingenjör

Molekylär cellbiologi

B-A317

Sölvegatan 35, Lund

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