dorsal/arxiv
View SchemaA Novel Approach to Structure Alignment
| Authors | M. Ohlsson, C. Peterson, M. Ringner, R. Blankenbecler |
|---|---|
| Categories | |
| ArXiv ID | physics/0006045 |
| URL | https://arxiv.org/abs/physics/0006045 |
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.
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"abstract": "A novel approach for structure alignment is presented, where the key\ningredients are: (1) An error function formulation of the problem\nsimultaneously in terms of binary (Potts) assignment variables and real-valued\natomic coordinates. (2) Minimization of the error function by an iterative\nmethod, where in each iteration a mean field method is employed for the\nassignment variables and exact rotation/translation of atomic coordinates is\nperformed, weighted with the corresponding assignment variables. The approach\nallows for extensive search of all possible alignments, including those\ninvolving arbitrary permutations. The algorithm is implemented using a C_alpha\nrepresentation of the backbone and explored on different protein structure\ncategories using the Protein Data Bank (PDB) and is successfully compared with\nother algorithms. The approach performs very well with modest CPU consumption\nand is robust with respect to choice of parameters. It is extremely generic and\nflexible and can handle additional user-prescribed constraints easily.\nFurthermore, it allows for a probabilistic interpretation of the results.",
"arxiv_id": "physics/0006045",
"authors": [
"M. Ohlsson",
"C. Peterson",
"M. Ringner",
"R. Blankenbecler"
],
"categories": [
"physics.bio-ph"
],
"title": "A Novel Approach to Structure Alignment",
"url": "https://arxiv.org/abs/physics/0006045"
},
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