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Progress on an open source computer-assisted structure elucidation suite (SENECA)

We suggested and developed various components for Computer-Assisted Structure Elucidation (CASE) over the years [1, 2]. Our current goal is to integrate these into an easy to use and efficient platform for end users, called SENECA. This is based on Bioclipse [3], an integrated software suite for chemo- and bioinformatics providing plugins for file handling and visualisation of compounds and spectra.

The SENECA feature currently comprises the following components and algorithms:

• A deterministic structure generator suitable for small chemical spaces.

• Simulated Annealing and Genetic Algorithm for random structure walks in large spaces.

Simulation of 13C NMR spectra for ranking results.

SENECA is a Bioclipse feature, available via the update site at http://www.ebi.ac.uk/steinbeck-srv/speclipse/net.bioclipse.seneca-updatesite/.

References

  1. 1.

    Steinbeck C, Krause S, Kuhn S: NMRShiftDB - Constructing a free chemical information system with open-source components. Journal of Chemical Information and Computer Sciences. 2003, 43: 1733-1739.

    CAS  Google Scholar 

  2. 2.

    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.

    Article  Google Scholar 

  3. 3.

    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.

    Article  Google Scholar 

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Correspondence to Stefan Kuhn.

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Kuhn, S., Steinbeck, C. Progress on an open source computer-assisted structure elucidation suite (SENECA). J Cheminform 2, P34 (2010). https://doi.org/10.1186/1758-2946-2-S1-P34

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Keywords

  • Genetic Algorithm
  • Structure Generator
  • Simulated Annealing
  • Open Source
  • Large Space