Geodesic
DomGen-Graph based method for protein domain delineation
Milostan, Maciej1 ; Lukasiak, Piotr1, 2
1 Poznan University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965 Poznan, Poland
2 Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland
RAIRO - Operations Research - Recherche Opérationnelle, Special issue: Research on Optimization and Graph Theory dedicated to COSI 2013 / Special issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine, Tome 50 (2016) no. 2, pp. 363-374

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The role of a protein depends heavily on its 3D shape, which is composed of semi-independent three-dimensional blocks called domains. Domains fold independently and constitute units of evolution. Most proteins contain multiple domains that are associated with a particular functions; moreover, the same domain can be found in different proteins. Automated recognition of domains can make prediction of proteins function easier and can support the analysis of proteins. Here, we propose a novel algorithm designed for domain recognition by identification of domain boundaries in the protein structure. The proposed algorithm uses a contact graph and an iterative approach to find meaningful clusters corresponding to the protein domains. The distinctive feature of the method is its effective complexity, that improves over other well-known methods, while holding a comparable level of correct domain assignments.

Reçu le :
Accepté le :
DOI : 10.1051/ro/2015040
Classification : 68R10, 92-08
Keywords: Graph theory, computational biology, protein structure

Milostan, Maciej 1 ; Lukasiak, Piotr 1, 2

1 Poznan University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965 Poznan, Poland
2 Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland 
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     author = {Milostan, Maciej and Lukasiak, Piotr},
     title = {DomGen-Graph based method for protein domain delineation},
     journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
     pages = {363--374},
     publisher = {EDP-Sciences},
     volume = {50},
     number = {2},
     year = {2016},
     doi = {10.1051/ro/2015040},
     mrnumber = {3479876},
     language = {en},
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}
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AU  - Lukasiak, Piotr
TI  - DomGen-Graph based method for protein domain delineation
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%D 2016
%P 363-374
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%I EDP-Sciences
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Milostan, Maciej; Lukasiak, Piotr. DomGen-Graph based method for protein domain delineation. RAIRO - Operations Research - Recherche Opérationnelle, Special issue: Research on Optimization and Graph Theory dedicated to COSI 2013 / Special issue: Recent Advances in Operations Research in Computational Biology, Bioinformatics and Medicine, Tome 50 (2016) no. 2, pp. 363-374. doi: 10.1051/ro/2015040

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