Progress on an open source computer-assisted structure elucidation suite (SENECA)
Journal of Cheminformatics volume 2, Article number: P34 (2010)
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 , 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/.
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.
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.
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.
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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
- Genetic Algorithm
- Structure Generator
- Simulated Annealing
- Open Source
- Large Space