Online bioinformatics teaching practice: Comparison of popular docking programs using SARS-CoV-2 spike RBD-ACE2...

Area of Science:

• Bioinformatics
• Computational Biology
• Molecular Biology

Background:

• The integration of bioinformatics and experimental biology is crucial for analyzing large biological datasets.
• Current bioinformatics education often emphasizes theory over practical application, leaving students unprepared for research.
• The COVID-19 pandemic created a need for remote, hands-on learning experiences in scientific fields.

Purpose of the Study:

• To present a bioinformatics docking project conducted by undergraduate students during COVID-19 self-isolation.
• To systematically compare open-source online molecular docking programs using the SARS-CoV-2 RBD-ACE2 complex as a benchmark.
• To provide students with practical experience in bioinformatics tools and collaborative research.

Main Methods:

• Students utilized the Receptor-Binding Domain (RBD) of the SARS-CoV-2 spike protein and its receptor, Angiotensin-Converting Enzyme 2 (ACE2), as a model system.
• A systematic comparison of several open-source online molecular docking programs was performed.
• Predicted molecular structures from docking simulations were compared against the known crystal structure.

Main Results:

• Students gained practical skills in using various bioinformatics docking tools.
• The project facilitated collaborative research and independent learning among students.
• The comparison provided insights into the performance of different open-source molecular docking programs.

Conclusions:

• Online workshops and practical projects are effective for teaching modern bioinformatics techniques.
• This approach allows students to engage with state-of-the-art computational biology and stay current with research trends.
• The project demonstrates how to transform learning challenges, like pandemic-related isolation, into valuable educational opportunities.