E1DS

catalytic site prediction based on 1D signatures of concurrent conservation.

Ting Ying Chien, Tien-Hao Chang, Chien Yu Chen, Yi Zhong Weng, Chen Ming Hsu

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Large-scale automatic annotation of protein sequences remains challenging in postgenomics era. E1DS is designed for annotating enzyme sequences based on a repository of 1D signatures. The employed sequence signatures are derived using a novel pattern mining approach that discovers long motifs consisted of several sequential blocks (conserved segments). Each of the sequential blocks is considerably conserved among the protein members of an EC group. Moreover, a signature includes at least three sequential blocks that are concurrently conserved, i.e. frequently observed together in sequences. In other words, a sequence signature is consisted of residues from multiple regions of the protein sequence, which echoes the observation that an enzyme catalytic site is usually constituted of residues that are largely separated in the sequence. E1DS currently contains 5421 sequence signatures that in total cover 932 4-digital EC numbers. E1DS is evaluated based on a collection of enzymes with catalytic sites annotated in Catalytic Site Atlas. When compared to the famous pattern database PROSITE, predictions based on E1DS signatures are considered more sensitive in identifying catalytic sites and the involved residues. E1DS is available at http://e1ds.ee.ncku.edu.tw/ and a mirror site can be found at http://e1ds.csbb.ntu.edu.tw/.

Original languageEnglish
JournalNucleic acids research
Volume36
Issue numberWeb Server issue
DOIs
Publication statusPublished - 2008 Jan 1

Fingerprint

Catalytic Domain
Enzymes
Molecular Sequence Annotation
Atlases
Proteins
Databases

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Chien, Ting Ying ; Chang, Tien-Hao ; Chen, Chien Yu ; Weng, Yi Zhong ; Hsu, Chen Ming. / E1DS : catalytic site prediction based on 1D signatures of concurrent conservation. In: Nucleic acids research. 2008 ; Vol. 36, No. Web Server issue.
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E1DS : catalytic site prediction based on 1D signatures of concurrent conservation. / Chien, Ting Ying; Chang, Tien-Hao; Chen, Chien Yu; Weng, Yi Zhong; Hsu, Chen Ming.

In: Nucleic acids research, Vol. 36, No. Web Server issue, 01.01.2008.

Research output: Contribution to journalArticle

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AU - Chang, Tien-Hao

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