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Reverse engineering chemical structures from molecular descriptors: how many solutions?

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Summary

Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

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Acknowledgements

This work was funded in part by the U.S. Department of Energy’s Genomics: GTL program (www.doegenomestolife.org) under project, “Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling” (www.genomes-to-life.org). This work was also funded by Sandia National Laboratories Computer Science Research Fund. Sandia is a multiprogram laboratory operated by Sandia Corporation, a LockheedMartin Company, for the United States Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

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Authors and Affiliations

  1. Computational Bioscience, Sandia National Laboratories, 969, Livermore, CA, 94551-9292, USA

    Jean-Loup Faulon

  2. Computational Biology, Sandia National Laboratories, 5800, Albuquerque, NM, 87185-0310, USA

    W. Michael Brown & Shawn Martin

Authors
  1. Jean-Loup Faulon
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  2. W. Michael Brown
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  3. Shawn Martin
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Correspondence to Jean-Loup Faulon.

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Faulon, JL., Brown, W.M. & Martin, S. Reverse engineering chemical structures from molecular descriptors: how many solutions?. J Comput Aided Mol Des 19, 637–650 (2005). https://doi.org/10.1007/s10822-005-9007-1

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  • DOI: https://doi.org/10.1007/s10822-005-9007-1

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