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Title 

DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture

Authors 

ByungUk LeeD Lee

Publisher 

Oxford University Press

Issue Date 

2008

Citation 

Nucleic Acids Research, vol. 36, no. Sup 2, pp. W60-W64

Keywords 

computer interfacecomputer programprotein tertiary structurestructural homologyprotein structure, tertiarysoftwarestructural homology, proteinuser-computer interface

Abstract 

We present DAhunter, a web-based server that identifies homologous proteins by comparing domain architectures, the organization of protein domains. A major obstacle in comparison of domain architecture is the existence of 'promiscuous' domains, which carry out auxiliary functions and appear in many unrelated proteins. To distinguish these promiscuous domains from protein domains, we assigned a weight score to each domain extracted from RefSeq proteins, based on its abundance and versatility. A domain's score represents its importance in the 'protein world' and is used in the comparison of domain architectures. In scoring domains, DAhunter also considers domain combinations as well as single domains. To measure the similarity of two domain architectures, we developed several methods that are based on algorithms used in information retrieval (the cosine similarity, the Goodman-Kruskal gamma function, and domain duplication index) and then combined these into a similarity score. Compared with other domain architecture algorithms, DAhunter is better at identifying homology.

ISSN 

0305-1048

Link 

http://dx.doi.org/10.1093/nar/gkn172

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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