DomGen-Graph based method for protein domain delineation
RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 363-374.

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.

Received:
Accepted:
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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Milostan, Maciej; Lukasiak, Piotr. DomGen-Graph based method for protein domain delineation. RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 363-374. doi : 10.1051/ro/2015040. http://archive.numdam.org/articles/10.1051/ro/2015040/

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