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  • Poster presentation
  • Open Access

Components for computer-assisted structure elucidation

  • 1,
  • 1 and
  • 1
Chemistry Central Journal20093 (Suppl 1) :P62

  • Published:


  • Genetic Algorithm
  • Natural Product
  • Structure Generator
  • Simulated Annealing
  • Search Engine

Computer-Assisted Structure Elucidation (CASE) is of relevance for various fields in chemistry and biology such as natural products discovery or metabolomics. Here we report on several software components developed in our team over time which can form part of an integrated CASE package. We aim to design a user-friendly and flexible, yet powerful tool with Bioclipse [1] as the frontend. Bioclipse is an integrated software suite for chemo- and bioinformatics providing plug-ins for file handling and visualisation of compounds and spectra. Spectrum look-up and prediction is provided by our open NMR database NMRShiftDB [2], offering both 13C and 1H NMR prediction. We have recently demonstrated the prediction of proton NMR spectra based on NMRShiftDB data with an average error of 0.18 ppm [3]. The resulting CASE system will provide a choice of different structure generators, including stochastic search engines, based on Simulated Annealing and Genetic Algorithms.

Authors’ Affiliations

Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK


  1. Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, et al: Bioclipse: An open source workbench for chemo- and bioinformatics. BMC Bioinformatics. 2007, 8: 59-10.1186/1471-2105-8-59.View ArticleGoogle Scholar
  2. Steinbeck C, Krause S, Kuhn S: NMRShiftDB – Constructing a free chemical information system with open-source components. J Chem Inf Comp Sci. 2003, 43: 1733-1739.View ArticleGoogle Scholar
  3. Kuhn S, Egert B, Neumann S, Steinbeck C: Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction. BMC Bioinformatics. 2008, 9: 400-10.1186/1471-2105-9-400.View ArticleGoogle Scholar


© Kuhn et al; licensee BioMed Central Ltd. 2009

This article is published under license to BioMed Central Ltd.