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Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions

Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions

Kateryna V. Miroshnychenko, Anna V. Shestopalova
Copyright: © 2016 |Pages: 31
ISBN13: 9781522503620|ISBN10: 1522503625|EISBN13: 9781522503637
DOI: 10.4018/978-1-5225-0362-0.ch005
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MLA

Miroshnychenko, Kateryna V., and Anna V. Shestopalova. "Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions." Applied Case Studies and Solutions in Molecular Docking-Based Drug Design, edited by Siavoush Dastmalchi, et al., IGI Global, 2016, pp. 127-157. https://doi.org/10.4018/978-1-5225-0362-0.ch005

APA

Miroshnychenko, K. V. & Shestopalova, A. V. (2016). Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions. In S. Dastmalchi, M. Hamzeh-Mivehroud, & B. Sokouti (Eds.), Applied Case Studies and Solutions in Molecular Docking-Based Drug Design (pp. 127-157). IGI Global. https://doi.org/10.4018/978-1-5225-0362-0.ch005

Chicago

Miroshnychenko, Kateryna V., and Anna V. Shestopalova. "Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions." In Applied Case Studies and Solutions in Molecular Docking-Based Drug Design, edited by Siavoush Dastmalchi, Maryam Hamzeh-Mivehroud, and Babak Sokouti, 127-157. Hershey, PA: IGI Global, 2016. https://doi.org/10.4018/978-1-5225-0362-0.ch005

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Abstract

Molecular docking of ligands to DNA-targets is of great importance for the design of new anticancer drugs. Unfortunately, most docking programs were developed for protein-ligand docking which raises a question about their applicability for the DNA-ligand docking. In this study, the popular docking programs AutoDock Vina, AutoDock4 and AutoDock3 were compared for a test set of 50 DNA-ligand complexes taken from the Nucleic Acid Database. It was shown that the version 3.05 of the AutoDock program was the most successful in reproducing the structures of intercalation and minor-groove complexes. The program AutoDock4 was able to re-dock to within 2 Å RMSD most of the intercalation complexes of the test set, but showed poor performance for minor groove binders. While Vina, on the contrary, failed to construct six intercalation complexes of the test set, but showed satisfactory results for DNA-ligand minor-groove complexes when small search space was used.

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