Presentation Title

Scripting to Save Time: Automating Virtual Screening

Faculty Mentor

P. Matthew Joyner

Start Date

17-11-2018 8:30 AM

End Date

17-11-2018 10:30 AM

Location

CREVELING 56

Session

POSTER 1

Type of Presentation

Poster

Subject Area

biological_agricultural_sciences

Abstract

Many drugs are small organic molecules that block an active site of a protein; however, the discovery process that identifies these small molecules takes extensive amounts of time, effort, and resources. We hypothesize that the virtual screening process can be streamlined by using scripts and freely available software to increase its efficiency and accessibility. Virtual screening is computationally analyzing large databases of small molecules to test the binding affinity to a receptor. There is free software, such as AutoDock Vina, available to conduct virtual screening. These programs save resources and laboratory time by narrowing down thousands to millions of compounds to those most likely to succeed as drug candidates. The current problem is that this virtual screening process is tedious and takes tremendous amounts of time that could be better used analyzing and confirming results with laboratory experiments. After researching potential software to use, it was determined that AutoDock Vina and DSX were the best freely available docking and scoring programs available. Windows Powershell scripts and bash scripts for Linux were designed and created to open, modify, and convert files, as well as to run each file through the software AutoDock Vina, and to acquire and compile scoring functions from DSX into a spreadsheet. Using these scripts reduces about 100 hours of active work to a few minutes of active work and 2-3 hours of computational time for a database of 1500 compounds. This is especially valuable for undergraduate students, graduate students, or other researchers who do not want to spend vast amounts of time or money on virtual screening. Since these scripts can be used for any protein that has a structure file in a protein database and any set of small molecules with structure files, there is a myriad of questions that can be explored using these scripts.

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Nov 17th, 8:30 AM Nov 17th, 10:30 AM

Scripting to Save Time: Automating Virtual Screening

CREVELING 56

Many drugs are small organic molecules that block an active site of a protein; however, the discovery process that identifies these small molecules takes extensive amounts of time, effort, and resources. We hypothesize that the virtual screening process can be streamlined by using scripts and freely available software to increase its efficiency and accessibility. Virtual screening is computationally analyzing large databases of small molecules to test the binding affinity to a receptor. There is free software, such as AutoDock Vina, available to conduct virtual screening. These programs save resources and laboratory time by narrowing down thousands to millions of compounds to those most likely to succeed as drug candidates. The current problem is that this virtual screening process is tedious and takes tremendous amounts of time that could be better used analyzing and confirming results with laboratory experiments. After researching potential software to use, it was determined that AutoDock Vina and DSX were the best freely available docking and scoring programs available. Windows Powershell scripts and bash scripts for Linux were designed and created to open, modify, and convert files, as well as to run each file through the software AutoDock Vina, and to acquire and compile scoring functions from DSX into a spreadsheet. Using these scripts reduces about 100 hours of active work to a few minutes of active work and 2-3 hours of computational time for a database of 1500 compounds. This is especially valuable for undergraduate students, graduate students, or other researchers who do not want to spend vast amounts of time or money on virtual screening. Since these scripts can be used for any protein that has a structure file in a protein database and any set of small molecules with structure files, there is a myriad of questions that can be explored using these scripts.