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A novel approach to structure alignment

Ohlsson, Mattias LU orcid ; Peterson, Carsten LU ; Ringnér, Markus LU orcid and Blankenbecler, Richard (2000) In LU TP 00-07
Abstract
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach allows for extensive search of all possible alignments, including those involving arbitrary permutations. The algorithm is implemented using a C_alpha representation of the backbone and explored on different protein structure... (More)
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach allows for extensive search of all possible alignments, including those involving arbitrary permutations. The algorithm is implemented using a C_alpha representation of the backbone and explored on different protein structure categories using the Protein Data Bank (PDB) and is successfully compared with other algorithms. The approach performs very well with modest CPU consumption and is robust with respect to choice of parameters. It is extremely generic and flexible and can handle additional user-prescribed constraints easily. Furthermore, it allows for a probabilistic interpretation of the results. (Less)
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author
; ; and
organization
publishing date
type
Book/Report
publication status
published
subject
in
LU TP 00-07
pages
18 pages
DOI
10.48550/arXiv.physics/0006045
language
English
LU publication?
yes
id
0e5b519d-e72f-4366-8c51-b1a29e0dadab (old id 4933220)
alternative location
https://www.slac.stanford.edu/pubs/slacpubs/8250/slac-pub-8429.pdf
date added to LUP
2016-04-04 13:02:27
date last changed
2022-05-14 02:17:42
@techreport{0e5b519d-e72f-4366-8c51-b1a29e0dadab,
  abstract     = {{A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach allows for extensive search of all possible alignments, including those involving arbitrary permutations. The algorithm is implemented using a C_alpha representation of the backbone and explored on different protein structure categories using the Protein Data Bank (PDB) and is successfully compared with other algorithms. The approach performs very well with modest CPU consumption and is robust with respect to choice of parameters. It is extremely generic and flexible and can handle additional user-prescribed constraints easily. Furthermore, it allows for a probabilistic interpretation of the results.}},
  author       = {{Ohlsson, Mattias and Peterson, Carsten and Ringnér, Markus and Blankenbecler, Richard}},
  language     = {{eng}},
  series       = {{LU TP 00-07}},
  title        = {{A novel approach to structure alignment}},
  url          = {{https://lup.lub.lu.se/search/files/118026311/4933231.pdf}},
  doi          = {{10.48550/arXiv.physics/0006045}},
  year         = {{2000}},
}