Reaction Similarities Focusing Substructure Changes of Chemical Compounds and Metabolic Pathway Alignments
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- Tohsato Yukako
- Department of Bioscience and Bioinformatics, College of Life Sciences, Ritsumeikan University
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- Nishimura Yu
- Information Science and Systems Engineering, Graduate School of Science and Engineering, Ritsumeikan University
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抄録
Comparative analyses of enzymatic reactions provide important information on both evolution and potential pharmacological targets. Previously, we focused on the structural formulae of compounds, and proposed a method to calculate enzymatic similarities based on these formulae. However, with the proposed method it is difficult to measure the reaction similarity when the formulae of the compounds constituting each reaction are completely different. The present study was performed to extract substructures that change within chemical compounds using the RPAIR data in KEGG. Two approaches were applied to measure the similarity between the extracted substructures: a fingerprint-based approach using the MACCS key and the Tanimoto/Jaccard coefficients; and the Topological Fragment Spectra-based approach that does not require any predefined list of substructures. Whether the similarity measures can detect similarity between enzymatic reactions was evaluated. Using one of the similarity measures, metabolic pathways in Escherichia coli were aligned to confirm the effectiveness of the method.
収録刊行物
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- IPSJ Transactions on Bioinformatics
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IPSJ Transactions on Bioinformatics 2 15-24, 2009
一般社団法人 情報処理学会
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詳細情報 詳細情報について
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- CRID
- 1390282680272201600
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- NII論文ID
- 130000122803
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- NII書誌ID
- AN00116647
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- ISSN
- 18827772
- 18826679
- 03875806
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- NDL書誌ID
- 024340223
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- NDL
- Crossref
- CiNii Articles
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- 使用不可