Current Drug Targets

Francis J. Castellino
Kleiderer-Pezold Professor of Biochemistry
Director, W.M. Keck Center for Transgene Research
Dean Emeritus, College of Science
230 Raclin-Carmichael Hall, University of Notre Dame
Notre Dame, IN 46556
USA

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Chemical Structure Similarity Search for Ligand-based Virtual Screening: Methods and Computational Resources

Author(s): Xin Yan, Chenzhong Liao, Zhihong Liu, Arnold T. Hagler, Qiong Gu, Jun Xu.

Graphical Abstract:


Abstract:

For many years the assumption that “Chemical compounds with similar structures may have similar activities” has been a foundation for lead identification. The similarity can be computed based upon topological, steric, electronic, and/or physical properties. The chemical structure similarity search differs from the chemical substructure search in that the former requires assessment of the properties of each compound and thus no filter can be applied for skipping structures before they are assessed to accelerate the computation. The latter can be accelerated by pre-screening compounds and omitting those that miss one (or more) specified fragments from the query. Moreover, three-dimensional similarity search requires superimposing many conformation pairs for each compound in the library. This makes 3-D similarity search algorithms time-consuming, and in general requires high performance computing (HPC) resources. This review will summarize recent progress in the techniques for HPC-supported two and three-dimensional chemical structure similarity search algorithms, and their applications in ligand-based virtual screening.

Keywords: Chemoinformatics, drug discovery, HPC, ligand-based virtual screening, structure similarity search.

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Article Details

VOLUME: 17
ISSUE: 14
Year: 2016
Page: [1580 - 1585]
Pages: 6
DOI: 10.2174/1389450116666151102095555
Price: $58