MD simulation tutorials (MD教程)

• MD workshop titled “Introduction to Molecular Dynamics Simulation: Theory and Practical Applications” (Aug 26, 2024 at NTU)
  Material on Github

• Build protein aggregation systems and mutate your protein using VMD (Link)

Python tutorials (Python教程)

• Try these Jupyter notebooks from your browser (JupyterLab environment provided by QuTiP; great learning material for beginners)

  • Introduction to Python (nbviewer)

  • Introduction to NumPy Arrays (nbviewer)

  • Plotting in Python using Matplotlib (nbviewer)

  Quick online launch —> Click “Try QuTiP from your browser“ botton there to launch —> JupyterLab (on your web browser) —> tutorials (folder) —> python-introduction (folder)

Background & Philosophy (背景知識與哲理)

You will easily learn some background knowledge and the philosophy of the lab by watching the video clips below. Grab a cup of coffee and enjoy!

Overview

• Animations of unseeable biology (TED talk by Drew Berry)

• The wonders of the molecular world (TED talk by Janet Iwasa)

Biochemistry (生化方面)

• What is a Protein? (from PDB 101, RCSB Protein Data Bank)

• What is Protein Folding? (from PDB 101, RCSB Protein Data Bank)

• The protein folding revolution (by Science Magazine, AAAS)

• Time-lapse of a nascent protein (by Chris Spronk and Barth van Rossum, Spronk Studio)

Molecular Dynamics Simulation (MD)

• The machinery underlying MD simulation (by Schrodinger TV)

Programming(程式方面)

• Which programming language should you learn in computational chemistry? (from the Science Addicted channel)

• The Linux command line (book by William Shotts)

Funny Applications(有趣的應用)

• Translating proteins into music, and back (from Markus Buehler lab in MIT)