title: A structural hierarchy matching approach for molecular similarity/substructure searching.
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.
authors.affiliation: Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. shushenjijss@163.com.
authors.forename: Shu-Shen
authors.initials: SS
authors.lastname: Ji
authors.affiliation: School of Life Sciences, Jilin University, Changchun 130012, China. hongju_dong@jlu.edu.cn.
authors.forename: Hong-Ju
authors.initials: HJ
authors.lastname: Dong
authors.affiliation: School of Chinese Pharmacy, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. gzzx@gzucm.edu.cn.
authors.forename: Xin-Xin
authors.initials: XX
authors.lastname: Zhou
authors.affiliation: The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. liuyamin2009@gzucm.edu.cn.
authors.forename: Ya-Min
authors.initials: YM
authors.lastname: Liu
authors.affiliation: Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. zhangfengxue@gzucm.edu.cn.
authors.forename: Feng-Xue
authors.initials: FX
authors.lastname: Zhang
authors.affiliation: Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. wangqi@gzucm.edu.cn.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Tropical Medicine Institute, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. xahuang@chinmednetworks.org.|South China Chinese Medicine Collaborative Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China. xahuang@chinmednetworks.org.
authors.forename: Xin-An
authors.initials: XA
authors.lastname: Huang
mesh_terms: D000465:Algorithms; D062126:Databases, Chemical; D015394:Molecular Structure; D013329:Structure-Activity Relationship
keywords: similarity searching; structural hierarchies; substructure searching