Abstract
Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described.
Key words
- Virtual molecular screening
- Computer-aided drug design
- Molecular docking
- PubChem
- AutoDock
- Vina
- Open Babel
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Acknowledgements
This work was supported by National Institute of Health (NIH) grant R01GM069832. The authors are very grateful to all those who contributed software used in this chapter. We also would like to thank Alex L. Perryman, Oleg Trott, Ruth Huey, and all members of our laboratories for helpful comments and discussions. This is manuscript # 25035 from The Scripps Research Institute.
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Dallakyan, S., Olson, A.J. (2015). Small-Molecule Library Screening by Docking with PyRx. In: Hempel, J., Williams, C., Hong, C. (eds) Chemical Biology. Methods in Molecular Biology, vol 1263. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2269-7_19
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DOI: https://doi.org/10.1007/978-1-4939-2269-7_19
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