License: Creative Commons Attribution-NoDerivs 3.0 Unported license (CC BY-ND 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/OASIcs.GCB.2012.23
URN: urn:nbn:de:0030-drops-37157
URL: https://drops.dagstuhl.de/opus/volltexte/2012/3715/
Go to the corresponding OASIcs Volume Portal

Ludwig, Marcus ; Hufsky, Franziska ; Elshamy, Samy ; Böcker, Sebastian

Finding Characteristic Substructures for Metabolite Classes

pdf-format:
4.pdf (0.7 MB)

Abstract

We introduce a method for finding a characteristic substructure for a set of molecular structures. Different from common approaches, such as computing the maximum common subgraph, the resulting substructure does not have to be contained in its exact form in all input molecules. Our approach is part of the identification pipeline for unknown metabolites using fragmentation trees. Searching databases using fragmentation tree alignment results in hit lists containing compounds with large structural similarity to the unknown metabolite. The characteristic substructure of the molecules in the hit list may be a key structural element of the unknown compound and might be used as starting point for structure elucidation. We evaluate our method on different data sets and find that it retrieves essential substructures if the input lists are not too heterogeneous. We apply our method to predict structural elements for five unknown samples from Icelandic poppy.

BibTeX - Entry

@InProceedings{ludwig_et_al:OASIcs:2012:3715,
  author =	{Marcus Ludwig and Franziska Hufsky and Samy Elshamy and Sebastian B{\"o}cker},
  title =	{{Finding Characteristic Substructures for Metabolite Classes}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{23--38},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{Sebastian B{\"o}cker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2012/3715},
  URN =		{urn:nbn:de:0030-drops-37157},
  doi =		{10.4230/OASIcs.GCB.2012.23},
  annote =	{Keywords: metabolites, substructure prediction, mass spectrometry, FT-BLAST}
}

Keywords: metabolites, substructure prediction, mass spectrometry, FT-BLAST
Collection: German Conference on Bioinformatics 2012
Issue Date: 2012
Date of publication: 13.09.2012

DROPS-Home | Fulltext Search | Imprint | Privacy Published by LZI