# About *DomainParser*

*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. A two-domain decomposition
problem is solved by finding a cut of the network, which minimizes the
total cross-edge capacity (minimum cut). The classical
Ford-Fulkerson algorithm is used to find a minimum cut of a network.
For proteins with multiple domains, our algorithm repeatedly applies
the Ford-Fulkerson algorithm to bi-partition the network and forms a
partition tree until some stopping criteria are met. To deal with
networks with non-unique minimum cuts, we have extended the algorithm
to find all cuts, which achieve the minimum cross-edge capacity, using
an enumeration algorithm by Picard and Queyranne. The capability of
finding all minimum cuts of a network allows us to evaluate and rank a
decomposition based on more global properties of a domain, including
its compactness and three-dimensional shape; and hence improve the
quality of a decomposition. A post-processing step is used to merge
segments that may have been overcut, based on certain geometric and
physical properties of a domain.

The program *DomainParser* is copyrighted and is NOT in the
public domain. The authors of *DomainParser* make no
representations about the suitability of the software for any purpose.
It is provided "as is" without express or implied warranty. The authors
shall not be liable for any damages suffered by Licensee from the use
of this software.

## References:

Ying Xu, Dong Xu, and Harold N. Gabow.
Protein Domain Decomposition using a Graph-Theoretic Approach. *Bioinformatics*.
16:1091-1104. 2000.

Jun-tao Guo, Dongsup Kim, Dong Xu, and Ying Xu. "Improving the Performance of DomainParser for Structural Domain Partition using Neural Network",
*Nucleic Acids Research* 2003 Feb 1;31(3):944-52.

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