Use of bioinformatics

Use of bioinformatics in education  


Here another piece I posted on ResearchGate which I think is worthwhile reading https://www.researchgate.net/publication/339311520_Possible_examples_of_using_Bioinformatics_in_your_chemistry_or_biology_class

In this concept I described possible examples of bioinformatics which can be used at secondary school/college level.


This piece can serve as inspiration. I strongly believe that using bioinformatics will help students in getting a deeper understanding of rather abstract concepts like amino acids, peptides, proteins, secondary structure. The role of hydrophobicity in folding and binding mechanisms (and how 'we' all know this) becomes more understandable for students at this (undergraduate) level.

I asked ChatGPT about this topic and this is what I got back:Bioinformatics is a powerful tool that can enhance the understanding of abstract biochemical concepts in both chemistry and biology classes. Here are some possible examples of how bioinformatics can be integrated into your lessons:

1. Exploring Amino Acids and Protein Structures

  • Use databases like UniProt or PDB (Protein Data Bank) to analyze the sequence and structure of proteins.
  • Have students compare hydrophobic and hydrophilic amino acids and predict their role in protein folding.

2. Protein Secondary Structure Prediction

  • Use tools like PSIPRED or JPred to predict secondary structures (alpha helices, beta sheets) from a given amino acid sequence.
  • Relate these structures to their functions in real proteins.

3. Hydrophobicity and Protein Folding

  • Utilize Kyte-Doolittle hydrophobicity plots to visualize hydrophobic and hydrophilic regions.
  • Have students predict how proteins will fold in an aqueous environment.

4. Molecular Docking & Binding Mechanisms

  • Introduce AutoDock or SwissDock to study how ligands interact with protein binding sites.
  • Show how molecular interactions (hydrophobic vs. hydrophilic) determine binding affinity.

5. Comparative Genomics & Evolutionary Relationships

  • Use BLAST (Basic Local Alignment Search Tool) to compare protein sequences and identify homologous proteins across species.
  • Discuss how conserved sequences reflect functional importance.

...well by itself an interesting and more or less accurate response by ChatGPT, but in detail it is not that informative. For example the response gives no specifics (servers, links, info on how to use the various approaches etc.). It also misses for example the highly interesting tool "Heliquest" https://heliquest.ipmc.cnrs.fr/index.html and the "Hydrophic Moment Plot" approach based on Heliquest generated data https://www.mdpi.com/1422-0067/12/9/5577

A small list of suggestions for further reading (besides some excellent books):

Jeff Gauthier, Antony T Vincent, Steve J Charette, Nicolas Derome, A brief history of bioinformatics, Briefings in Bioinformatics, Volume 20, Issue 6, November 2019, Pages 1981–1996, https://doi.org/10.1093/bib/bby063

Min, S., Lee, B., & Yoon, S. (2017). Deep learning in bioinformatics. Briefings in bioinformatics, 18(5), 851-869.

Kanehisa, M., & Bork, P. (2003). Bioinformatics in the post-sequence era. Nature genetics, 33(3), 305-310.

Keller, R. C. A. (2011). New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis. International Journal of Molecular Sciences, 12(9), 5577-5591. https://doi.org/10.3390/ijms12095577


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