Response surface methodology in docking study of small molecule BACE-1 inhibitors.

Journal of Molecular Modeling
Nima Razzaghi-AslRamin Miri

Abstract

Computational evaluation of ligand-receptor binding via docking strategy is a well established approach in structure-based drug design. This technique has been applied frequently in developing molecules of biological interest. However, any procedure would require an optimization set up to be more efficient, economic and time-saving. Advantages of modern statistical optimization methods over conventional one-factor-at-a-time studies have been well revealed. The optimization by experimental design provides a combination of factor levels simultaneously satisfying the requirements considered for each of the responses and factors. In this study, response surface method was applied to optimize the prominent factors (number of genetic algorithm runs, population size, maximum number of evaluations, torsion degrees for ligand and number of rotatable bonds in ligand) in AutoDock4.2-based binding study of small molecule β-secretase inhibitors as anti-alzheimer agents. Results revealed that a number of rotatable bonds in ligand and maximum number of docking evaluations were determinant variables affecting docking outputs. The interference between torsion degrees for ligand and number of genetic algorithm runs for docking procedure was foun...Continue Reading

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Citations

Jan 28, 2017·Computational Biology and Chemistry·Fatemeh BohlooliNima Razzaghi-Asl
Aug 3, 2014·Journal of Biomolecular Screening·Vikramjeet SinghJingsong Zhu

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