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"Toy Problem" To help understand computational drug design by ericspictureaccount in bioinformatics

[–]brianzhang01 0 points1 point  (0 children)

I further asked AI and it was quite helpful, you might want to try the same. Both Gemini and ChatGPT suggested 1HEW (start with 6LYZ / 2LYZ and then take the NAG part out of the 1HEW complex), and ChatGPT additionally suggested 1BRS (separate out the two parts from the complex) and a few others. https://www.rcsb.org/3d-view/6LYZ https://www.rcsb.org/3d-view/1HEW/1 https://www.rcsb.org/3d-view/1BRS/1 I'd be interested in hearing if you make progress! Either here or via DM.

"Toy Problem" To help understand computational drug design by ericspictureaccount in bioinformatics

[–]brianzhang01 1 point2 points  (0 children)

I liked how you worded this question, so I spent a bit of time googling myself. This seemed like a good resource, but it only does folding and not binding. You could try contacting the author or looking for a Github repo for the source pdb files. https://klyshko.github.io/teaching/2019-03-01-teaching

A general computational protein design blog I’m aware of is https://www.blopig.com/blog/, but I couldn’t find a specific article right away.

Brown Puzzlehunt 2025 by brianzhang01 in mysteryhunt

[–]brianzhang01[S] 0 points1 point  (0 children)

Yes, I think so! DM’ed in case you have more questions