DomGen-Graph based method for protein domain delineation^∗

¹ Poznan University of Technology, Institute of Computing Science, ul. Piotrowo 2, 60-965 Poznan, Poland
mmilostan@cs.put.poznan.pl; plukasiak@cs.put.poznan.pl
² Institute of Bioorganic Chemistry, Polish Academy of Sciences, ul. Noskowskiego 12/14, 61-704 Poznan, Poland

Received: 8 September 2015
Accepted: 21 September 2015

Abstract

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.