Automation of the <i>Ad Hoc</i> Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences

Abstract

Data analysis and manipulation software are vulnerable to user error during data processing and computations take considerable time when handling huge data and multiple repetitive tasks. These problems are usually mitigated by creating an app to repeat any given task reproducibly any number of times. This paper discusses the development of app that systematically automates the <i>ad hoc</i> approach for derandomization of proteins and, or peptides. Thirty second-year undergraduates with little-to-no prior knowledge of computer programming are (were) asked to create this app with modules that sequentially convert spectra from original units to molar extinction and subtract baseline spectrum from the resultant spectra, derandomize the spectra by removing suspected significant unfolded domains from them, concatenate the generated files to a single file in an acceptable format for structural analysis, process our group structural algorithm output files into a user-friendly format to ease data analysis. In addition, they are (were) asked to prepare protein solution, determine its concentration spectroscopically, collect circular dichroism measurements of the protein, derandomize the protein spectra, and determine the secondary structure of the resultant protein spectra with our structure algorithm. The assessment results demonstrated that the students could prepare samples for CD analysis, collect spectra of proteins, and create an app to automate the <i>ad hoc</i> approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.