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

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 consis...

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Detalles Bibliográficos
Autores principales: Chien, Ting-Ying, Chang, Darby Tien-Hao, Chen, Chien-Yu, Weng, Yi-Zhong, Hsu, Chen-Ming
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447799/
https://www.ncbi.nlm.nih.gov/pubmed/18524800
http://dx.doi.org/10.1093/nar/gkn324
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author Chien, Ting-Ying
Chang, Darby Tien-Hao
Chen, Chien-Yu
Weng, Yi-Zhong
Hsu, Chen-Ming
author_facet Chien, Ting-Ying
Chang, Darby Tien-Hao
Chen, Chien-Yu
Weng, Yi-Zhong
Hsu, Chen-Ming
author_sort Chien, Ting-Ying
collection PubMed
description 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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spelling pubmed-24477992008-07-09 E1DS: catalytic site prediction based on 1D signatures of concurrent conservation Chien, Ting-Ying Chang, Darby Tien-Hao Chen, Chien-Yu Weng, Yi-Zhong Hsu, Chen-Ming Nucleic Acids Res Articles 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/. Oxford University Press 2008-07-01 2008-06-04 /pmc/articles/PMC2447799/ /pubmed/18524800 http://dx.doi.org/10.1093/nar/gkn324 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Articles
Chien, Ting-Ying
Chang, Darby Tien-Hao
Chen, Chien-Yu
Weng, Yi-Zhong
Hsu, Chen-Ming
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title_full E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title_fullStr E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title_full_unstemmed E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title_short E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
title_sort e1ds: catalytic site prediction based on 1d signatures of concurrent conservation
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447799/
https://www.ncbi.nlm.nih.gov/pubmed/18524800
http://dx.doi.org/10.1093/nar/gkn324
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