Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Giv...

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Autores principales:	Yu-Fei Gao, Lei Chen, Yu-Dong Cai, Kai-Yan Feng, Tao Huang, Yang Jiang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b12904116dc642fcaf89a50fd1c6f409
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spelling	oai:doaj.org-article:b12904116dc642fcaf89a50fd1c6f4092021-11-18T07:04:28ZPredicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.1932-620310.1371/journal.pone.0045944https://doaj.org/article/b12904116dc642fcaf89a50fd1c6f4092012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23029334/?tool=EBIhttps://doaj.org/toc/1932-6203Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.Yu-Fei GaoLei ChenYu-Dong CaiKai-Yan FengTao HuangYang JiangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e45944 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yu-Fei Gao Lei Chen Yu-Dong Cai Kai-Yan Feng Tao Huang Yang Jiang Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
description	Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.
format	article
author	Yu-Fei Gao Lei Chen Yu-Dong Cai Kai-Yan Feng Tao Huang Yang Jiang
author_facet	Yu-Fei Gao Lei Chen Yu-Dong Cai Kai-Yan Feng Tao Huang Yang Jiang
author_sort	Yu-Fei Gao
title	Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
title_short	Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
title_full	Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
title_fullStr	Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
title_full_unstemmed	Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
title_sort	predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/b12904116dc642fcaf89a50fd1c6f409
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_version_	1718424000400457728

Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

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