Lots of discussion on plagiarism. But to me, it seems that people we should be really trying to punish for this are also the people that you can't detect via simple text matching. I'm talking about "plagiarism of ideas" either from pre-prints or conferences or discussion etc. 🤔
It's all about biasing AF to sample the alt state... sometimes multiple methods will work for a different reasons, it doesn't mean one is better than the other. Ironically, "cf-random" is invoking AF's internal clustering... 😅 so it is NOT a good "control" to test if clustering helps or not. (2/2)
I dont think there is a single method that works for all cases. It really depends on the MSA. If there are pockets of seqs that prefer one state vs other, then af-cluster can help. If both states are equally preferred and there is coevolutio signal for both, subsampling or col masking can help (1/2)
Not sure yet... Still waiting on the room preparation. 😅
At #NeurIPS2023 this week! Reach out if you wanna meet up. 😎🧬🖥️
Learn how to predict mono-, multi-mers and conformations with our ColabFold/AlphaFold2 protocol. It covers workflows for beginners as well as advanced concepts. Great work by Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim @agsmith.bsky.social@sokrypton.org@milot.bsky.social
But back to our paper... we explore this question in the SI, and actually take advantage of the fact that single sequence is sometimes enough to design a new protein where a few point mutations switch to the alternative conformation. 🤓 (8/8) www.nature.com/articles/s41...
Besides the examples where it's sometimes possible to predict from single sequence. There have been other examples where it was not possible. If it is memorization, why would AF memorize one example and not another? 🤔 twitter.com/GMondaSilva/... (7/8)
