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Nucleic Acids Research Advance Access published online on June 4, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn324
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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E1DS: catalytic site prediction based on 1D signatures of concurrent conservation

Ting-Ying Chien1, Darby Tien-Hao Chang2,*, Chien-Yu Chen3, Yi-Zhong Weng1 and Chen-Ming Hsu4

1Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, 2Department of Electrical Engineering, National Cheng Kung University, Tainan 701, 3Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 106 and 4Department of Computer Science and Engineering, Yuan Ze University, Chung-Li 320, Taiwan, ROC

*To whom correspondence should be addressed. Tel: +886 6 2757575 62421; Fax: +886 6 2345482; Email: darby{at}ee.ncku.edu.tw

Received February 3, 2008. Revised April 25, 2008. Accepted May 7, 2008.

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/.


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D. T.-H. Chang, T.-Y. Chien, and C.-Y. Chen
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[Abstract] [Full Text] [PDF]


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