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

Adewale Olamoyesan

doi:doi:10.11648/j.ijctc.20241201.13

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

Adewale Olamoyesan

Published in International Journal of Computational and Theoretical Chemistry (Volume 12, Issue 1)

Received: 24 May 2024 Accepted: 15 June 2024 Published: 27 June 2024

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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 ad hoc 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 ad hoc approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.

Published in	International Journal of Computational and Theoretical Chemistry (Volume 12, Issue 1)
DOI	10.11648/j.ijctc.20241201.13
Page(s)	18-23
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

MATLAB, Application, Second-Year Undergraduate, Circular Dichroism, Protein

References

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[9]	Fisher, A. A., An Introduction to Coding with Matlab: Simulation of X-ray Photoelectron Spectroscopy by Employing Slater’s Rules. Journal of Chemical Education. 2019, 96, 1502-1505. https://doi.org/10.1021/acs.jchemed.9b00236
[10]	Hall, V., Nash, A., Rodger, A. SSNN, A Method for Neural Network Protein Secondary Structure Fitting Using Circular Dichroism Data. Analytical Methods. 2014, 6(17), 6721-6726. https://doi.org/10.1039/c3ay41831f
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[14]	Olamoyesan, A., Ang, D., Rodger, A. Circular Dichroism for Secondary Structure Determination of Proteins with Unfolded Domains Using a Self-organising Map Algorithm SOMSpec. RSC Advances 2021, 11 (39), 23985-23991. https://doi.org/10.1039/ d1ra02898g
[15]	Olamoyesan, A., Rodger, A. Application of Derandomisation to Peptide Circular Dichroism Spectra to Determine their Secondary Structure Content. South African. Journal Chemistry. 2024, 78, 52–60. https://doi.org/10.17159/0379-4350/2024/v78a10
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APA Style

Olamoyesan, A. (2024). Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. International Journal of Computational and Theoretical Chemistry, 12(1), 18-23. https://doi.org/10.11648/j.ijctc.20241201.13

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ACS Style

Olamoyesan, A. Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. Int. J. Comput. Theor. Chem. 2024, 12(1), 18-23. doi: 10.11648/j.ijctc.20241201.13

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AMA Style

Olamoyesan A. Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. Int J Comput Theor Chem. 2024;12(1):18-23. doi: 10.11648/j.ijctc.20241201.13

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@article{10.11648/j.ijctc.20241201.13,
  author = {Adewale Olamoyesan},
  title = {Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences
},
  journal = {International Journal of Computational and Theoretical Chemistry},
  volume = {12},
  number = {1},
  pages = {18-23},
  doi = {10.11648/j.ijctc.20241201.13},
  url = {https://doi.org/10.11648/j.ijctc.20241201.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20241201.13},
  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 ad hoc 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 ad hoc approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.
},
 year = {2024}
}

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TY  - JOUR
T1  - Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences

AU  - Adewale Olamoyesan
Y1  - 2024/06/27
PY  - 2024
N1  - https://doi.org/10.11648/j.ijctc.20241201.13
DO  - 10.11648/j.ijctc.20241201.13
T2  - International Journal of Computational and Theoretical Chemistry
JF  - International Journal of Computational and Theoretical Chemistry
JO  - International Journal of Computational and Theoretical Chemistry
SP  - 18
EP  - 23
PB  - Science Publishing Group
SN  - 2376-7308
UR  - https://doi.org/10.11648/j.ijctc.20241201.13
AB  - 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 ad hoc 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 ad hoc approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.

VL  - 12
IS  - 1
ER  -

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Author Information

Adewale Olamoyesan

Department of Molecular Sciences, Macquarie University, Sydney, Australia; Department of Chemistry, University of Lagos, Lagos, Nigeria; College of Science and Computing, Wigwe University, Isiokpo, Nigeria

Contact Email

http://orcid.org/0000-0002-9879-6726

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Plain Text BibTeX RIS

APA Style

Olamoyesan, A. (2024). Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. International Journal of Computational and Theoretical Chemistry, 12(1), 18-23. https://doi.org/10.11648/j.ijctc.20241201.13

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ACS Style

Olamoyesan, A. Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. Int. J. Comput. Theor. Chem. 2024, 12(1), 18-23. doi: 10.11648/j.ijctc.20241201.13

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AMA Style

Olamoyesan A. Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences. Int J Comput Theor Chem. 2024;12(1):18-23. doi: 10.11648/j.ijctc.20241201.13

Copy | Download

@article{10.11648/j.ijctc.20241201.13,
  author = {Adewale Olamoyesan},
  title = {Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences
},
  journal = {International Journal of Computational and Theoretical Chemistry},
  volume = {12},
  number = {1},
  pages = {18-23},
  doi = {10.11648/j.ijctc.20241201.13},
  url = {https://doi.org/10.11648/j.ijctc.20241201.13},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijctc.20241201.13},
  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 ad hoc 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 ad hoc approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.
},
 year = {2024}
}

Copy | Download

TY  - JOUR
T1  - Automation of the Ad Hoc Approach for Derandomization of Proteins: A Tutorial for Undergraduates in Molecular Sciences

AU  - Adewale Olamoyesan
Y1  - 2024/06/27
PY  - 2024
N1  - https://doi.org/10.11648/j.ijctc.20241201.13
DO  - 10.11648/j.ijctc.20241201.13
T2  - International Journal of Computational and Theoretical Chemistry
JF  - International Journal of Computational and Theoretical Chemistry
JO  - International Journal of Computational and Theoretical Chemistry
SP  - 18
EP  - 23
PB  - Science Publishing Group
SN  - 2376-7308
UR  - https://doi.org/10.11648/j.ijctc.20241201.13
AB  - 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 ad hoc 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 ad hoc approach. The hands-on activities enable students to acquire knowledge in basic programming and circular dichroism, CD spectroscopy.

VL  - 12
IS  - 1
ER  -

Copy | Download