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A Novel Approach to Structure Alignment

Ohlsson, Mattias LU ; Peterson, Carsten LU ; Ringnér, Markus LU and Blankenbecler, Richard (2000) In Preprint without journal information
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
organization
publishing date
type
Contribution to journal
publication status
unpublished
subject
in
Preprint without journal information
pages
18 pages
publisher
Manne Siegbahn Institute
ISSN
0348-7911
language
English
LU publication?
yes
id
0e5b519d-e72f-4366-8c51-b1a29e0dadab (old id 4933220)
date added to LUP
2015-01-12 13:55:08
date last changed
2016-10-10 16:12:29
@misc{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},
  issn         = {0348-7911},
  language     = {eng},
  pages        = {18},
  publisher    = {ARRAY(0x9318618)},
  series       = {Preprint without journal information},
  title        = {A Novel Approach to Structure Alignment},
  year         = {2000},
}