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Matching protein structures with fuzzy alignments

Blankenbecler, R; Ohlsson, Mattias LU ; Peterson, Carsten LU and Ringnér, Markus LU (2003) In Proceedings of the National Academy of Sciences 100(21). p.11936-11940
Abstract
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,... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
algorithm, mean field annealing, fuzzy assignment, dynamical programming
in
Proceedings of the National Academy of Sciences
volume
100
issue
21
pages
11936 - 11940
publisher
National Acad Sciences
external identifiers
  • wos:000186024300005
  • scopus:0142091424
ISSN
1091-6490
DOI
10.1073/pnas.1635048100
language
English
LU publication?
yes
id
6a889c84-01f4-4222-b7d1-0a5139befa90 (old id 297515)
date added to LUP
2007-08-24 11:41:58
date last changed
2018-05-29 10:41:10
@article{6a889c84-01f4-4222-b7d1-0a5139befa90,
  abstract     = {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.},
  author       = {Blankenbecler, R and Ohlsson, Mattias and Peterson, Carsten and Ringnér, Markus},
  issn         = {1091-6490},
  keyword      = {algorithm,mean field annealing,fuzzy assignment,dynamical programming},
  language     = {eng},
  number       = {21},
  pages        = {11936--11940},
  publisher    = {National Acad Sciences},
  series       = {Proceedings of the National Academy of Sciences},
  title        = {Matching protein structures with fuzzy alignments},
  url          = {http://dx.doi.org/10.1073/pnas.1635048100},
  volume       = {100},
  year         = {2003},
}