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Title: Efficient enumeration of monocyclic chemical graphs with given path frequencies.
Authors: Suzuki, Masaki
Nagamochi, Hiroshi  kyouindb  KAKEN_id
Akutsu, Tatsuya  kyouindb  KAKEN_id
Author's alias: 永持, 仁
Keywords: Chemical graphs
Enumeration
Monocyclic structure
Feature vector
Issue Date: 30-May-2014
Publisher: Chemistry Central
Journal title: Journal of cheminformatics
Volume: 6
Thesis number: 31
Abstract: [Background]The enumeration of chemical graphs (molecular graphs) satisfying given constraints is one of the fundamental problems in chemoinformatics and bioinformatics because it leads to a variety of useful applications including structure determination and development of novel chemical compounds. [Results]We consider the problem of enumerating chemical graphs with monocyclic structure (a graph structure that contains exactly one cycle) from a given set of feature vectors, where a feature vector represents the frequency of the prescribed paths in a chemical compound to be constructed and the set is specified by a pair of upper and lower feature vectors. To enumerate all tree-like (acyclic) chemical graphs from a given set of feature vectors, Shimizu et al. and Suzuki et al. proposed efficient branch-and-bound algorithms based on a fast tree enumeration algorithm. In this study, we devise a novel method for extending these algorithms to enumeration of chemical graphs with monocyclic structure by designing a fast algorithm for testing uniqueness. The results of computational experiments reveal that the computational efficiency of the new algorithm is as good as those for enumeration of tree-like chemical compounds.[Conclusions] We succeed in expanding the class of chemical graphs that are able to be enumerated efficiently.
Rights: © 2014 Suzuki et al.; licensee Chemistry Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
URI: http://hdl.handle.net/2433/188897
DOI(Published Version): 10.1186/1758-2946-6-31
PubMed ID: 24955135
Appears in Collections:Journal Articles

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