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Carsten Peterson

Expert

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Matching protein structures with fuzzy alignments

Författare

  • 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.

Avdelning/ar

  • Computational Biology and Biological Physics - Undergoing reorganization

Publiceringsår

2003-10-14

Språk

Engelska

Sidor

11936-11940

Publikation/Tidskrift/Serie

Proceedings of the National Academy of Sciences

Volym

100

Issue

21

Dokumenttyp

Artikel i tidskrift

Förlag

National Academy of Sciences

Ämne

  • Biophysics

Nyckelord

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

Aktiv

Published

ISBN/ISSN/Övrigt

  • ISSN: 1091-6490