Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Published online before print October 14, 2003, 10.1101/gr.1212003
Genome Res. 13:2455-2466, 2003
©2003 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/03 $5.00
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
1212003v1
13/11/2455    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Arita, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Arita, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Methods

In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism

Masanori Arita

Department of Computational Biology, Faculty of Frontier Sciences, The University of Tokyo and PRESTO, JST, 277-8561 Kashiwa, Japan

We present a software system that computationally reproduces biochemical radioisotope-tracer experiments. It consists of three main components: A mapping database of substrate-product atomic correspondents derived from known reaction formulas, a tracing engine that can compute all pathways between two given compounds by using the mapping database, and a graphical user interface. As the system can facilitate the display of all possible pathways between any two compounds and the tracing of every single carbon, nitrogen, or sulfur atom in the metabolism, it complements and bridges other metabolic databases and simulations on fixed models.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1212003. Article published online before print in October 2003.

[The software and data files for the Escherichia coli metabolism (MOL-format files for molecular structures, reaction formulas for enzymes, and mapping information at the atomic level) are available at http://www.metabolome.jp/.]


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
F. Mu, R. F. Williams, C. J. Unkefer, P. J. Unkefer, J. R. Faeder, and W. S. Hlavacek
Carbon-fate maps for metabolic reactions
Bioinformatics, December 1, 2007; 23(23): 3193 - 3199.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Ogata and J.-M. Claverie
Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D321 - D324.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. Arita
The metabolic world of Escherichia coli is not small
PNAS, February 10, 2004; 101(6): 1543 - 1547.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
Y. Yamazaki, M. Kitajima, M. Arita, H. Takayama, H. Sudo, M. Yamazaki, N. Aimi, and K. Saito
Biosynthesis of Camptothecin. In Silico and in Vivo Tracer Study from [1-13C]Glucose
Plant Physiology, January 1, 2004; 134(1): 161 - 170.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.
Copyright © 2003 by Cold Spring Harbor Laboratory Press.