Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information | Zendy

Sunghoon Lee | Zendy; Bora Lee | Zendy; In Sock Jang | Zendy; Semi Kim | Zendy; Jong Bhak | Zendy

Open Access

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information

Author(s) -

Sunghoon Lee,

Bora Lee,

In Sock Jang,

Semi Kim,

Jong Bhak

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl351

Subject(s) - topology (electrical circuits) , network topology , transmembrane domain , domain (mathematical analysis) , representation (politics) , computer science , transmembrane protein , biology , computational biology , protein domain , helix (gastropod) , membrane protein , data mining , bioinformatics , genetics , gene , computer network , mathematics , combinatorics , membrane , mathematical analysis , receptor , ecology , politics , political science , snail , law

The Localizome server predicts the transmembrane (TM) helix number and TM topology of a user-supplied eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains and a prediction algorithm, Phobius, to predict the TM helices. The results are combined and checked against the TM topology rules stored in a protein domain database called LocaloDom. LocaloDom is a curated database that contains TM topologies and TM helix numbers of known protein domains. It was constructed from Pfam domains combined with Swiss-Prot annotations and Phobius predictions. The Localizome server corrects the combined results of the user sequence to conform to the rules stored in LocaloDom. Compared with other programs, this server showed the highest accuracy for TM topology prediction: for soluble proteins, the accuracy and coverage were 99 and 75%, respectively, while for TM protein domain regions, they were 96 and 68%, respectively. With a graphical representation of TM topology and TM helix positions with the domain units, the Localizome server is a highly accurate and comprehensive information source for subcellular localization for soluble proteins as well as membrane proteins. The Localizome server can be found at http://localizome.org/.

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