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

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      Author(s): 1 , , 1
      Publication date (Electronic):
      Journal: Journal of Cheminformatics
      Publisher: BioMed Central
      Conference name: 5th German Conference on Cheminformatics: 23. CIC-Workshop
      Conference date: 8–10 November 2009

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          Abstract

          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/.

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          Bioclipse: an open source workbench for chemo- and bioinformatics

          Ola Spjuth, Tobias Helmus, Egon Willighagen … (2007)
          Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at .
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            NMRShiftDB-constructing a free chemical information system with open-source components.

            Christoph Steinbeck, Stefan Krause, Stefan Kuhn (2015)
            The process of designing and implementing NMRShiftDB, an open-source, open-content database for chemical structures and their NMR data based solely on free software is described. NMRShiftDB is available to the community on http://www.nmrshiftdb.org. It allows for open submission and retrieval of data sets by its user community. The software and the content itself is freely distributable, allowing for the establishment of a highly available mirror system of databases in collaborating laboratories.
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              Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction

              Stefan Kuhn, Björn Egert, Steffen Neumann … (2008)
              Background Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances and measurements of their concentration. Still, only a fraction of existing metabolites and their spectral fingerprints are known. Computer-Assisted Structure Elucidation (CASE) of biological metabolites will be an important tool to leverage this lack of knowledge. Indispensable for CASE are modules to predict spectra for hypothetical structures. This paper evaluates different statistical and machine learning methods to perform predictions of proton NMR spectra based on data from our open database NMRShiftDB. Results A mean absolute error of 0.18 ppm was achieved for the prediction of proton NMR shifts ranging from 0 to 11 ppm. Random forest, J48 decision tree and support vector machines achieved similar overall errors. HOSE codes being a notably simple method achieved a comparatively good result of 0.17 ppm mean absolute error. Conclusion NMR prediction methods applied in the course of this work delivered precise predictions which can serve as a building block for Computer-Assisted Structure Elucidation for biological metabolites.
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                Author and article information

                Conference
                Journal ID (nlm-ta): J Cheminform
                Title: Journal of Cheminformatics
                Publisher: BioMed Central
                ISSN (Electronic): 1758-2946
                Publication date Collection: 2010
                Publication date (Electronic): 4 May 2010
                Volume: 2
                Issue: Suppl 1
                Page: P34
                Affiliations
                [1 ]Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Article
                Publisher ID: 1758-2946-2-S1-P34
                DOI: 10.1186/1758-2946-2-S1-P34
                PMC ID: 2867168
                SO-VID: 3e03806b-8140-47cb-956f-eeb3299efaee
                Copyright © Copyright ©2010 Stefan and Christoph; licensee BioMed Central Ltd.
                Conference name: 5th German Conference on Cheminformatics: 23. CIC-Workshop
                Conference location: Goslar, Germany
                Conference date: 8–10 November 2009
                History
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                Subject: Poster Presentation

                ScienceOpen disciplines: Chemoinformatics
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                ScienceOpen disciplines: Chemoinformatics

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