Comments L3

[raquellrios]

Comments:

• Slide 7 should mention that the bound and docked ligands need to be sufficiently similar for shape-based docking methods to work effectively.
• (Optional) The image quality on slide 9 is not very good, would it be possible to improve it?
• On slide 15 I would clarify that the RMSD is measured relative to the crystal/reference structure, some students may not know this. Also, are we assuming students know what is the RMSD? The first lecture starts from very simple concepts (what is a protein), so I would add a concise definition of RSMD on this slide or slide 13. This would ensure all students can follow along, even without a lecture.
• (Optional) Slide 17 includes "things to worry about", I think it would be good to add a sentence about what is the impact of not considering these things properly in the docking calculations.
• On slide 20 I would highlight the tools that are open source
• (Optional) On slide 21 maybe list 2 advantages of ML-based docking over traditional methods (and 2 disadvantages)
• Overall I really like the graphical explanations of this Lecture ❤️

[raquellrios]

Practical 3:

• (Optional) I think adding a visualization cell of the protein and ligand that the students are going to dock after getting it from the PDB would enhance the students' understanding of the steps they are taking.
• Really like the "Questions to think about" and visualization of the docking grid ❤️