Skip to main content
Download PDF
Download ePub

Volume 2 Supplement 1

5th German Conference on Cheminformatics: 23. CIC-Workshop

  • Poster presentation
  • Open access
  • Published:

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

Journal of Cheminformatics volume 2, Article number: P34 (2010) Cite this article

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. 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. 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. 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 

Download references

Author information

Authors and Affiliations

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

    Stefan Kuhn & Christoph Steinbeck

Authors
  1. Stefan Kuhn
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Christoph Steinbeck
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License ( https://creativecommons.org/licenses/by-nc/2.0 ), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.

Reprints and permissions

About this article

Cite this article

Kuhn, S., Steinbeck, C. Progress on an open source computer-assisted structure elucidation suite (SENECA). J Cheminform 2 (Suppl 1), P34 (2010). https://doi.org/10.1186/1758-2946-2-S1-P34

Download citation

  • Published:

  • DOI: https://doi.org/10.1186/1758-2946-2-S1-P34

Keywords

Journal of Cheminformatics

ISSN: 1758-2946

Contact us