Display Settings:

Format

Send to:

Choose Destination
PLoS One. 2012;7(9):e45944. doi: 10.1371/journal.pone.0045944. Epub 2012 Sep 21.

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

Author information

  • 1Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.

Erratum in

  • PLoS One. 2012;7(11):doi/10.1371/annotation/83922541-168a-4d4f-846a-cb5d127aa7a9.

Abstract

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.

PMID:
23029334
[PubMed - indexed for MEDLINE]
PMCID:
PMC3448724
Free PMC Article

Images from this publication.See all images (3)Free text

Figure 1
Figure 2
Figure 3
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Public Library of Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk