3 ms·

I feel that the "produced excellent results" has a lot of unpack there. It obviously wasn't scoring 90+ in CASP. Actually, after reading your linked blog post

I feel that the "produced excellent results" has a lot of unpack there. It obviously wasn't scoring 90+ in CASP. Actually, after reading your linked blog post, it's pretty obvious why they weren't exactly chomping on the bit: "To gain insights into the receptor’s dynamics, Kai performed detailed molecular simulations using hundreds of millions of core hours on Google’s infrastructure, generating hundreds of terabytes of valuable molecular dynamics data." Hmm, yes, hundreds of millions of hours of cpu time, hundreds of terabytes of data, who says no to that? It doesn't even seem seem to attack generalized protein folding in general. It really seems like the plan was, "let's attack this problem with a Google-sized firehose" rather than created a fundamentally different algorithm that had game-changing results. Comparing your system to AlphaFold seems like your really bending the truth here.

dekhn 6y ago
If you note, the paper has an enormous number of citations from pharma, since modelling protein dynamics, rather than static structure, is key to understsanding ligand binding firehose. You can see another paper we published where attacking the problem with a firehose helped unlock a long-standing problem: https://pubmed.ncbi.nlm.nih.gov/24265211/ https://pubmed.ncbi.nlm.nih.gov/24265211/ in this case, showed that bond angles need to be 'free' to move rather than fully constrained,to build the most accurate models. This paper is also heavily cited amongst protein modellers. It is correct that the MD simulations don't directly work for CASP- in a sense, the results they produce directly disagree with CASP's mental model of protein structure and function.