DomainParser uses a new algorithm for the decomposition of a multi-domain protein into individual structural domains. The underlying principle used is that residue-residue contacts are denser within a domain than between domains. We have formulated the domain decomposition problem as a network flow problem, in which each residue is represented as a node of a network and each residue-residue contact is represented as an edge with a particular capacity, depending on the type of the contact.
Dr. Ying Xu @ CSBL
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Ying Xu, Dong Xu, and Harold N. Gabow.
Protein Domain Decomposition using a Graph-Theoretic Approach.
Bioinformatics. 16:1091-1104. 2000.