Predicting biological functions of compounds based on chemical-chemical interactions.

Given a compound, how can we effectively predict its biological function? It is a fundamentally important problem because the information thus obtained may benefit the understanding of many basic biological processes and provide useful clues for drug design. In this study, based on the information o...

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Autores principales:	Le-Le Hu, Chen Chen, Tao Huang, Yu-Dong Cai, Kuo-Chen Chou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/afa3cbc93b2e466b9d0d443bcad47487
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spelling	oai:doaj.org-article:afa3cbc93b2e466b9d0d443bcad474872021-11-18T07:31:17ZPredicting biological functions of compounds based on chemical-chemical interactions.1932-620310.1371/journal.pone.0029491https://doaj.org/article/afa3cbc93b2e466b9d0d443bcad474872011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22220213/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Given a compound, how can we effectively predict its biological function? It is a fundamentally important problem because the information thus obtained may benefit the understanding of many basic biological processes and provide useful clues for drug design. In this study, based on the information of chemical-chemical interactions, a novel method was developed that can be used to identify which of the following eleven metabolic pathway classes a query compound may be involved with: (1) Carbohydrate Metabolism, (2) Energy Metabolism, (3) Lipid Metabolism, (4) Nucleotide Metabolism, (5) Amino Acid Metabolism, (6) Metabolism of Other Amino Acids, (7) Glycan Biosynthesis and Metabolism, (8) Metabolism of Cofactors and Vitamins, (9) Metabolism of Terpenoids and Polyketides, (10) Biosynthesis of Other Secondary Metabolites, (11) Xenobiotics Biodegradation and Metabolism. It was observed that the overall success rate obtained by the method via the 5-fold cross-validation test on a benchmark dataset consisting of 3,137 compounds was 77.97%, which is much higher than 10.45%, the corresponding success rate obtained by the random guesses. Besides, to deal with the situation that some compounds may be involved with more than one metabolic pathway class, the method presented here is featured by the capacity able to provide a series of potential metabolic pathway classes ranked according to the descending order of their likelihood for each of the query compounds concerned. Furthermore, our method was also applied to predict 5,549 compounds whose metabolic pathway classes are unknown. Interestingly, the results thus obtained are quite consistent with the deductions from the reports by other investigators. It is anticipated that, with the continuous increase of the chemical-chemical interaction data, the current method will be further enhanced in its power and accuracy, so as to become a useful complementary vehicle in annotating uncharacterized compounds for their biological functions.Le-Le HuChen ChenTao HuangYu-Dong CaiKuo-Chen ChouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 12, p e29491 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Le-Le Hu Chen Chen Tao Huang Yu-Dong Cai Kuo-Chen Chou Predicting biological functions of compounds based on chemical-chemical interactions.
description	Given a compound, how can we effectively predict its biological function? It is a fundamentally important problem because the information thus obtained may benefit the understanding of many basic biological processes and provide useful clues for drug design. In this study, based on the information of chemical-chemical interactions, a novel method was developed that can be used to identify which of the following eleven metabolic pathway classes a query compound may be involved with: (1) Carbohydrate Metabolism, (2) Energy Metabolism, (3) Lipid Metabolism, (4) Nucleotide Metabolism, (5) Amino Acid Metabolism, (6) Metabolism of Other Amino Acids, (7) Glycan Biosynthesis and Metabolism, (8) Metabolism of Cofactors and Vitamins, (9) Metabolism of Terpenoids and Polyketides, (10) Biosynthesis of Other Secondary Metabolites, (11) Xenobiotics Biodegradation and Metabolism. It was observed that the overall success rate obtained by the method via the 5-fold cross-validation test on a benchmark dataset consisting of 3,137 compounds was 77.97%, which is much higher than 10.45%, the corresponding success rate obtained by the random guesses. Besides, to deal with the situation that some compounds may be involved with more than one metabolic pathway class, the method presented here is featured by the capacity able to provide a series of potential metabolic pathway classes ranked according to the descending order of their likelihood for each of the query compounds concerned. Furthermore, our method was also applied to predict 5,549 compounds whose metabolic pathway classes are unknown. Interestingly, the results thus obtained are quite consistent with the deductions from the reports by other investigators. It is anticipated that, with the continuous increase of the chemical-chemical interaction data, the current method will be further enhanced in its power and accuracy, so as to become a useful complementary vehicle in annotating uncharacterized compounds for their biological functions.
format	article
author	Le-Le Hu Chen Chen Tao Huang Yu-Dong Cai Kuo-Chen Chou
author_facet	Le-Le Hu Chen Chen Tao Huang Yu-Dong Cai Kuo-Chen Chou
author_sort	Le-Le Hu
title	Predicting biological functions of compounds based on chemical-chemical interactions.
title_short	Predicting biological functions of compounds based on chemical-chemical interactions.
title_full	Predicting biological functions of compounds based on chemical-chemical interactions.
title_fullStr	Predicting biological functions of compounds based on chemical-chemical interactions.
title_full_unstemmed	Predicting biological functions of compounds based on chemical-chemical interactions.
title_sort	predicting biological functions of compounds based on chemical-chemical interactions.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/afa3cbc93b2e466b9d0d443bcad47487
work_keys_str_mv	AT lelehu predictingbiologicalfunctionsofcompoundsbasedonchemicalchemicalinteractions AT chenchen predictingbiologicalfunctionsofcompoundsbasedonchemicalchemicalinteractions AT taohuang predictingbiologicalfunctionsofcompoundsbasedonchemicalchemicalinteractions AT yudongcai predictingbiologicalfunctionsofcompoundsbasedonchemicalchemicalinteractions AT kuochenchou predictingbiologicalfunctionsofcompoundsbasedonchemicalchemicalinteractions
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Predicting biological functions of compounds based on chemical-chemical interactions.

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