상세 정보

underline
Metadata Downloads : dc(xml) or Excel
Cited 0 time in scopus ci

Title 

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

Authors 

Sung Hoon LeeByungUk LeeInsoo JangS KimJong Bhak

Publisher 

Oxford University Press

Issue Date 

2006

Citation 

Nucleic Acids Research, vol. 34, no. W, pp. w99-w103

Keywords 

membrane proteincell compartmentalizationcomputer interfacecomputer programeukaryotic cellevaluationprotein databaseprotein secondary structureprotein tertiary structurecell compartmentation

Abstract 

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/.

ISSN 

0305-1048

Link 

http://dx.doi.org/10.1093/nar/gkl351

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


Files in This Item: SizeFormat
6519.pdf448KbAdobe PDF
qrcode

FusionCharts.
DSpace Software Coptright(c) 2010 MIT and Hewleft-Packard  /  KRIBB-REPOSITORY ( Email:jakim@kribb.re.kr)