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Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures

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Summary

Substructural fragments are proposed as a simple and safe way to encode molecular structures in a matrix containing the occurrence of fragments of a given type. The knowledge retrieved from QSPR modelling can also be stored in that matrix in addition to the information about fragments. Complex supramolecular systems (using special bond types) and chemical reactions (represented as Condensed Graphs of Reactions, CGR) can be treated similarly. The efficiency of fragments as descriptors has been demonstrated in QSPR studies of aqueous solubility for a diverse set of organic compounds as well as in the analysis of thermodynamic parameters for hydrogen-bonding in some supramolecular complexes. It has also been shown that CGR may be an interesting opportunity to perform similarity searches for chemical reactions. The relationship between the density of information in descriptors/knowledge matrices and the robustness of QSPR models is discussed.

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Acknowledgement

GDR PARIS and GDRE SupraChem are acknowledged for support. FH thanks Novalyst Discovery for a PhD fellowship.

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Authors and Affiliations

  1. Laboratoire d’Infochimie, UMR 7551 CNRS, Université Louis Pasteur, 4, rue B., 67000, Pascal, Strasbourg, France

    A. Varnek, D. Fourches & F. Hoonakker

  2. Institute of Physical Chemistry, Russian Academy of Sciences, Leninskiy Prosp. 31a, 119991 Moscow, Russia

    V. P. Solov’ev

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  1. A. Varnek
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  2. D. Fourches
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  3. F. Hoonakker
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  4. V. P. Solov’ev
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Correspondence to A. Varnek.

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Varnek, A., Fourches, D., Hoonakker, F. et al. Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures. J Comput Aided Mol Des 19, 693–703 (2005). https://doi.org/10.1007/s10822-005-9008-0

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  • DOI: https://doi.org/10.1007/s10822-005-9008-0

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