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Bytes of BioWelcome to Bytes of Bio, a podcast where we explain Bioinformatics, an effective combination between Computer Science and Biology. We're May and Allamanda or Allie for short. Welcome to our show! So glad to have you here! We upload every 3 weeks on... Author: May
Welcome to Bytes of Bio, a podcast where we explain Bioinformatics, an effective combination between Computer Science and Biology. We're May and Allamanda or Allie for short. Welcome to our show! So glad to have you here! We upload every 3 weeks on Sundays. Hope to see you then! Language: en Genres: Science Contact email: Get it Feed URL: Get it iTunes ID: Get it |
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Episode 5 - Stimulate the Simulation
Sunday, 30 December, 2018
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 interactionMolecular 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.If you like this episode please leave a rating or a review!
