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Toolbox: CATALOGIC-Soil BioPath
Potential use:
An extension of biodegradation CATALOGIC models enabling predicting biodegradation pathways in soil.
Novelty and background:
vDatabase of observed biodegradation pathways for 183 chemicals, mainly pesticides was used to build the model.  Substances with a variety of chemical functionality, such as acid amides, aniline and nitrobenzenes, dithio and thiolcarbamates, five- and six-rings heterocyclic compounds, phenyl (aryl) carbamates, phosphoro(di)thiolates, sulfonylureas, etc. are presented in the database.  Metabolic fate of chemicals is simulated via the principal molecular transformations extracted from the metabolic pathway database.  The molecular transformation consists of parent sub-molecular fragment, transformation products and inhibiting functional groups.  The hierarchy of the transformations and their probabilities are used to control the propagation of the catabolic maps of the chemicals. 
Description of tool:
The tool is ready for use.  It is part of models implemented on the platform CATALOGIC for environmental models developed by LMC. The only required input information is molecular structure (SMILES, InChi, or other codes for 2D structure). Model output consists of predicted sequence of metabolites that are expected to be observed in soil.  The model is accompanied with fully searchable electronic database of documented metabolism in soil.  An upgraded new version of the model is planned to be released once per year.
Current state:
ready to use
  1. NoMiracle IP D.2.3.12 Report on first prototype of model for predicting biodegradation pathways in soil.
  2. Dimitrov S, Nedelcheva D, Dimitrova N, Mekenyan, O. Predicting biodegradation of chemicals in soil. Presented at the 17th Annual Meeting of SETAC Europe, May 20-24, 2007, Porto, Portugal. (poster).
  3. Dimitrov S, NoMiracle Workshop on Integrated Assessment of Environmental and Human Health, Frankfurt, Germany, 8-9 September, 2008 (platform).
  4. Dimitrov S, Nedelcheva D, Dimitrova N, Mekenyan O, (submitted) Development of a biodegradation model for the prediction of metabolites in soil Sci Total Environ.
Responsible scientists:
Prof. Ovanes Mekenyan, Ph. D., D. Sci.
Department of Physical Chemistry
Laboratory of Mathematical Chemistry, Head
Bourgas "Prof. As. Zlatarov" University "Yakimov" St. #1 8010 Bourgas Bulgaria
phone: ++359 56 880230 (also personal fax)
++359 56 858343
fax: ++359 56 880249
LMC website:
Related to deliverable:
Tool box Soil BioPath LMC.doc