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Authors: Fei He ; Akiyoshi Hanai ; Hiroshi Nagamochi and Tatsuya Akutsu

Affiliation: Kyoto University, Japan

ISBN: 978-989-758-170-0

Keyword(s): Isomers Enumeration, Naphthalene, Chemical Graph.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Immuno- and Chemo-Informatics

Abstract: In this paper, we consider the problem of enumerating naphthalene isomers, where enumeration of isomers is important for drug design. A chemical graph G with no other cycles than naphthalene rings is called tree-like, and becomes a tree T possibly with multiple edges if we contract each naphthalene ring into a single virtual atom of valence 8. We call tree T the tree representation of G. There may be more than one tree-like chemical graphs whose tree representations equal to T, which are called naphthalene isomers of T. We present an efficient algorithm that enumerates all naphthalene isomers of a given tree representation. Our algorithm first counts the number of all the naphthalene isomers using dynamic programming, and then for each k, generates the k-th isomer by backtracking the counting computation. In computational experiment, we compare our method with MolGen, a state-of-the-art enumeration tool, and it is observed that our program enumerates the same number of naphthalene iso mers within extremely shorter time, which proves that our algorithm is effectively built. (More)

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Paper citation in several formats:
He, F.; Hanai, A.; Nagamochi, H. and Akutsu, T. (2016). Enumerating Naphthalene Isomers of Tree-like Chemical Graphs.In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 258-265. DOI: 10.5220/0005783902580265

@conference{bioinformatics16,
author={Fei He. and Akiyoshi Hanai. and Hiroshi Nagamochi. and Tatsuya Akutsu.},
title={Enumerating Naphthalene Isomers of Tree-like Chemical Graphs},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)},
year={2016},
pages={258-265},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005783902580265},
isbn={978-989-758-170-0},
}

TY - CONF

JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2016)
TI - Enumerating Naphthalene Isomers of Tree-like Chemical Graphs
SN - 978-989-758-170-0
AU - He, F.
AU - Hanai, A.
AU - Nagamochi, H.
AU - Akutsu, T.
PY - 2016
SP - 258
EP - 265
DO - 10.5220/0005783902580265

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