Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach

J Chem Inf Model. 2008 Jun;48(6):1181-9. doi: 10.1021/ci7004324. Epub 2008 Jun 6.


Chemical reactions transform the reactant molecules by deleting existing and forming new bonds. The identification of these so-called reacting bonds is important for studying the reaction mechanism and for applications in metabolomics, e.g. for interpreting substrate labeling experiments. Here, we introduce an approach which suggests the simplest possible reaction center at the heavy atom level, with high accuracy. In contrast to current methods the approach is motivated by a simple theoretical model based on a crude approximation of the reaction energetics, and takes the complete reacting system into account. Finally, it recovers all optimal solutions to the problem while removing all symmetry-related, redundant solutions. We apply the method on the complete KEGG database of biochemical reactions, and compare our approach with previous methods. The resulting reaction centers are represented as imaginary transition states, which are molecule-like representations of reaction mechanisms. We provide the statistics of the calculations on the KEGG database and discuss some examples for the different types of alternative solutions found.

MeSH terms

  • Databases, Factual
  • Enzymes / chemistry
  • Enzymes / metabolism
  • Hydrogen / chemistry
  • Models, Chemical*
  • Sensitivity and Specificity
  • Thermodynamics


  • Enzymes
  • Hydrogen