Using Supercomputing to Conduct Virtual Screen as Part of the Drug Discovery Process in a Medicinal Chemistry Course

Volume 3, Issue 2 (December 2012), pp. 18–25

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@article{jocse-3-2-3,
  author={David Toth and Jimmy Franco},
  title={Using Supercomputing to Conduct Virtual Screen as Part of the Drug Discovery Process in a Medicinal Chemistry Course},
  journal={The Journal of Computational Science Education},
  year=2012,
  month=dec,
  volume=3,
  issue=2,
  pages={18--25},
  doi={https://doi.org/10.22369/issn.2153-4136/3/2/3}
}

The ever-increasing amount of computational power available has made it possible to use docking programs to screen large numbers of compounds to search for molecules that inhibit proteins. This technique can be used not only by pharmaceutical companies with large research and development budgets and large research universities, but also at small liberal arts colleges with no special computing equipment beyond the desktop PCs in any campus' computer laboratory. However, despite the availability of significant quantities of compute time available to small colleges to conduct these virtual screens, such as supercomputing time available through grants, we are unaware of any small colleges that do this. We describe the experiences of an interdisciplinary research collaboration between faculty in the Chemistry and Computer Science Departments in a chemistry course where chemistry and biology students were shown how to conduct virtual screens. This project began when the authors, who had been collaborating on drug discovery research using virtual screening, decided that the virtual screening process they were using in their research could be adapted to fit in a couple of lab periods and would complement one of the instructors' courses on medicinal chemistry. The resulting labs would introduce students to the virtual screening portion of the drug discovery process.