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.
Highlights
Structural fragments are commonly used for structural and similarity searches
The chemical environment information is limitedly given for the substructures, this approach offers an acceptable result on the matching precision tests, in which over
This approach conducts the substructure searching in two stages: conducting one-point, two-point, or multi-point searching and ranking the retrieved molecules using the hierarchy of the query as reference
Summary
Shu-Shen Ji 1, Hong-Ju Dong 2, Xin-Xin Zhou 3, Ya-Min Liu 4, Feng-Xue Zhang 1, Qi Wang 5,* and Xin-An Huang 1,6,*. South China Chinese Medicine Collaborative Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
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