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Open AccessCommunication
Molecules 2015, 20(5), 8791-8799; doi:10.3390/molecules20058791

A Structural Hierarchy Matching Approach for Molecular Similarity/Substructure Searching

1
Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
2
School of Life Sciences, Jilin University, Changchun 130012, China
3
School of Chinese Pharmacy, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
4
The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
5
Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
6
South China Chinese Medicine Collaborative Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
*
Authors to whom correspondence should be addressed.
Academic Editor: Derek J. McPhee
Received: 17 February 2015 / Revised: 11 May 2015 / Accepted: 12 May 2015 / Published: 15 May 2015
(This article belongs to the Section Molecular Diversity)
View Full-Text   |   Download PDF [303 KB, uploaded 19 May 2015]   |  

Abstract

An approach for molecular similarity/substructure searching based on structural hierarchy matching is proposed. In this approach, small molecules are divided into two categories, acyclic and cyclic forms. The latter are further divided into three structural hierarchies, namely, framework, complicated-, and mono-rings. During searching, the similarity coefficients of a structural query and each retrieved molecule are calculated using the hierarchy of the query as the reference. A total of 13,911 chemicals were involved in this work, from which the minimal cyclic and acyclic substructures are extracted, and further processed into fuzzy structural fingerprints. Subsequently, the fingerprints are used as the searching indices for molecular similarity or substructure searching. The tests show that this approach can give user options to choose between one-substructure and multi-substructure searching with sorted results. Moreover, this algorithm has the potential to be developed for molecular similarity searching and substructure analysis. View Full-Text
Keywords: similarity searching; substructure searching; structural hierarchies similarity searching; substructure searching; structural hierarchies
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Ji, S.-S.; Dong, H.-J.; Zhou, X.-X.; Liu, Y.-M.; Zhang, F.-X.; Wang, Q.; Huang, X.-A. A Structural Hierarchy Matching Approach for Molecular Similarity/Substructure Searching. Molecules 2015, 20, 8791-8799.

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