Episode 5 - Stimulate the Simulation - a podcast by May

Welcome to the 5th episode of Bytes of Bio, Stimulate the Simulation!

In between making babies with the Reaper and burning people alive, the Sims can actually teach you Bioinfo?

Let’s go through the main points we have discussed!
- Goal: Use simulation created by bioinformatics to study interactions between drugs and viruses. By doing so, we can determine the efficiency of drugs.
- Important definition:
Docking: how one molecule fits into another and interact with each other (binding energy, binding position, etc.)
Active sites: sites that make the virus active, or “brain” of the virus → the place the drug should bind to in order to inactivate the virus.
Peak: The location with the highest binding energy → signal the drug where the active site is.
- Steps:
Prep phase: prepare the “environment” for interaction
Molecular Dynamics: carry out simulation and record results.
Steepest descent algorithm: analyze the results using specific algorithms.
Partial least-squares regression: double-check results.
Mutual Info: filter out data to clarify and give better results.

Reference links mentioned throughout the podcast:
- Detailed procedure of prep phase (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm)
- Mutual Info (https://imgur.com/a/Tuet7RK)

Additional Information:
What is the reason behind we have to add hydrogen atoms during the protein optimization for molecular docking?
Answer: The addition of hydrogen helps to find the hydrogen bond interactions and more favorable to us to find binding affinity of ligand against protein.

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