Vittamin EP.1 "เรียนรู้สู้ COVID-19 ด้วย Bioinformatics"

By: Bundit Boonyarit, Ph.D. student Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC)

Date: March 22, 2020, 7:00 - 9.30 PM

For more information about me, please see https://manbaritone.com/

Lecture:

Part 1: https://youtu.be/sOc7mqKamTQ
Part 2: https://youtu.be/ypzd9TGjgJE

Files:

1. Presentation file
2. Try to Visualize Tutorial
   2.1 6LU7 PDB file
   2.2 6LU7 VMD file
3. Try to Dock Tutorial
   3.1 Tutorial folder
4. Similarity search in ChEMBL database
   4.1 similarity_search_for_compounds_ChEMBL.ipynb
   4.2 cov_compounds.csv
   4.3 cov_compounds.smi
   4.4 cov_compounds.mol2

Demo:

DEMO I: Try to Visualize with VMD

Visualizing 3C‐like serine protease (3CLpro) of SARS-CoV-2 with ligand by VMD and export illustration.

Material: PDB file (6Y2F)
Software: VMD

DEMO II: Try to Dock with DOCK 6

Docking 3C‐like serine protease (3CLpro) of SARS-CoV-2 with co-crystal ligand by DOCK 6 and retrieve similar ligands from ChEMBL database for virtual screening, which is executed by Google Colab

Material: PDB file (6Y2F)
Software: DOCK 6, Chimera
Platform: Google Colab

Credits:

1. Jiramet Kinchagawat, Dept. Bio and Brain Engineering, KAIST
2. Natthakan Saengnil, KVIS
3. Puri Virakarin, KVIS