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      CheS-Mapper - Chemical Space Mapping and Visualization in 3D

      , 1 , 1 , 2

      Journal of Cheminformatics

      BioMed Central

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          Abstract

          Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis.

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          Most cited references 11

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          Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

          The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.
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            The WEKA data miing software: an update

             M Hall,  E Frank,  G Holmes (2009)
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              Structure--activity landscape index: identifying and quantifying activity cliffs.

              A new method for analyzing a structure-activity relationship is proposed. By use of a simple quantitative index, one can readily identify "structure-activity cliffs": pairs of molecules which are most similar but have the largest change in activity. We show how this provides a graphical representation of the entire SAR, in a way that allows the salient features of the SAR to be quickly grasped. In addition, the approach allows us view the SARs in a data set at different levels of detail. The method is tested on two data sets that highlight its ability to easily extract SAR information. Finally, we demonstrate that this method is robust using a variety of computational control experiments and discuss possible applications of this technique to QSAR model evaluation.
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                Author and article information

                Journal
                J Cheminform
                J Cheminform
                Journal of Cheminformatics
                BioMed Central
                1758-2946
                2012
                17 March 2012
                : 4
                : 7
                Affiliations
                [1 ]Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
                [2 ]Institute for Computer Science, Johannes Gutenberg-Universität Mainz, Mainz, Germany
                Article
                1758-2946-4-7
                10.1186/1758-2946-4-7
                3331825
                22424447
                Copyright ©2012 Gütlein et al; licensee Chemistry Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Categories
                Software

                Chemoinformatics

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