Lately I've seen videos and some articles explaining drug design. I would also like to specifically cite this guy, who isn't the most credible guy in the planet, but some of the stuff in the video makes sense to some degree, and he just confused me further.
Now I work on a completely different field on my day job, but I would like to ask a few questions, out of curiosity, because the techniques described in the video really piqued my interest.
- Is it the case that when designing drugs (i.e. these proteins) we attempt to optimise binding affinity (maximise?)
- How well does Autodock Vina compute this affinity? Is it opinionated? I've seen a few docking software, it looks like there are different methods to compute docking score? (can you recommend further reading for me in this regard)
- Is there a linear correlation between binding affinity and drug efficacy? I.e. does it mean that higher binding affinity directly means we have a better drug, or is there some sweet point kinda thing?
- Why can't we use very complex molecules, more than 300 characters in SMILES length to combat viruses for example? I noticed everyone was trying to minimise ligands?
- How can software like AutoDock tools prepare your proteins for docking, is there a standard method (they add hydrogens, add Gasteiger charges). Is that guaranteed to be accurate in every case?
To clarify, I'm not looking for detailed answers, since I am completely off the domain, I just want to have a basic idea for these questions, and perhaps recommendations on further reading from you guys.
Thank you, and stay strong!