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DOI: 10.4230/LIPIcs.SEA.2026.15

Computational Generation of Substrate-Specific Molecular Cages

Authors: Noé Demange, Yann Strozecki, and Sandrine Vial

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract

In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a simple method to place binding patterns which are able to interact with certain parts of the substrate. We then propose an algorithm which considers all possible ways of connecting these binding patterns and try to construct the smallest possible molecular paths realizing these connections. We investigate many variants of our method in order to obtain the most efficient algorithm, able to build cages of more than a hundred atoms.

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Noé Demange, Yann Strozecki, and Sandrine Vial. Computational Generation of Substrate-Specific Molecular Cages. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 15:1-15:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{demange_et_al:LIPIcs.SEA.2026.15,
  author =	{Demange, No\'{e} and Strozecki, Yann and Vial, Sandrine},
  title =	{{Computational Generation of Substrate-Specific Molecular Cages}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{15:1--15:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.15},
  URN =		{urn:nbn:de:0030-drops-260191},
  doi =		{10.4230/LIPIcs.SEA.2026.15},
  annote =	{Keywords: Enumeration, Molecular Cage, Cheminformatics, Geometric Algorithms, Experimental Algorithms}
}

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Computational Generation of Substrate-Specific Molecular Cages

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