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Determining Similarity of Conformational Polymorphs

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Algorithms — ESA 2002 (ESA 2002)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2461))

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Abstract

Conformational polymorphs are identical molecules that crystallize in different spatial formations. Understanding the amount of difference between the polymorphs might aid drug design as there is a widespread assumption that there exists a direct connection between the conformations in the crystallized form of the molecule and the conformations in the solvent.

We define a measure of similarity between conformational polymorphs and present an algorithm to compute it. For this end we weave together in a novel way our graph isomorphism method and substructure matching. We tested our algorithm on conformational polymorphs from the Cambridge Structural Database. Our experiments show that our method is very efficient in practice and has already yielded an important insight on the polymorphs stored in the data base.

K. Kedem was supported by NSF CISE Research Infrastructure grant #EIA- 9972853, by NSF #CCR-9988519, and by a grant from the Israeli Defence Ministry.

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Author information

Authors and Affiliations

  1. Computer Science Department, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel

    Angela Enosh & Klara Kedem

  2. Chemistry Department, Ben-Gurion University of the Negev, 84105, Beer Sheva, Israel

    Joel Bernstein

Authors
  1. Angela Enosh
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  2. Klara Kedem
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  3. Joel Bernstein
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Editor information

Editors and Affiliations

  1. Fakultät II: Mathematik und Naturwissenschaften, Technische Universität Berlin, Strasse des 17. Juni 136, 10623, Berlin, Germany

    Rolf Möhring

  2. Department of Mathematics and Computer Science, University of Leicester, University Road, LE1 7RH, Leicester, UK

    Rajeev Raman

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© 2002 Springer-Verlag Berlin Heidelberg

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Enosh, A., Kedem, K., Bernstein, J. (2002). Determining Similarity of Conformational Polymorphs. In: Möhring, R., Raman, R. (eds) Algorithms — ESA 2002. ESA 2002. Lecture Notes in Computer Science, vol 2461. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45749-6_40

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  • DOI: https://doi.org/10.1007/3-540-45749-6_40

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44180-9

  • Online ISBN: 978-3-540-45749-7

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