lysozyme
Joined 5 years ago
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Comment · 2 years ago
It’s interesting how Egypt’s efforts to monitor and test for malaria contributed to this accomplishment. It underscores how eradicating many infectious diseases will require a deep understanding not only of the disease itself, but also the cycles of transmission and the complex ecology of different hosts.
Malaria’s complex lifecycle [1] seems like it would be easy to “break” with different interventions, but we’ve seen historically malaria has been difficult to eradicate. Why is this?
1. https://en.m.wikipedia.org/wiki/Plasmodium#/media/File%3ALif...
Comment · 2 years ago
For those like myself who design proteins for a living, the open secret is that well before AlphaFold, it was pretty much possible to get a good-enough structure of any particular protein you really cared about (from say 2005) by other means, namely Baker’s Rosetta.
I constantly use AlphaFold structures today [1]. And AlphaFold is fantastic. But it only replaces one small step in solving any real-world problem involving proteins such as designing a safe, therapeutic protein binder to interrupt cancer-associated protein-protein interactions or designing an enzyme to degrade PFAS.
I think the primary achievement is that it gets protein structures in front of a lot more smart eyes, and for a lot more proteins. For “everyone else” who never needed to master computational protein structure prediction workflows before, they now have easy access to the rich, function-determinative structural information they need to understand and solve their problem.
The real tough problem in protein design is how to use these structure predictions to understand and ultimately create proteins we care about.
1. https://alexcarlin.bearblog.dev/multistate-protein-design-wi...
Comment · 2 years ago
Agreed, the UX of a magnet timer on the fridge beats using any kind of smart device for the task of setting kitchen timers. Most of them start a simple count up if not programmed for a specific duration, so you can watch the seconds.
Most magnet timers also remember the last duration, so if you use the same timer a lot for the same task (tea, for example), it’s literally a single button press. The same operation on any kind of smart device contains a staggering number of steps, each of which requires cognition and attention.
Magnet timers are also super cheap, so you can get another one if you have two favorite durations. A simple solution meets a simple problem
Comment · 2 years ago
Agreed on the hopes that these methods lead to novel biocatalysts (but they aren’t quite there yet).
David Baker’s lab has recently published on using their own diffusion model (RFdiffusion) to design novel biocatalysts that perform hydrolysis using a catalytic triad of serine, aspartic acid, and histidine, as well as an oxyanion hole, which is much more complex than the binders designed by AlphaProteo [1].
It gives me hope that we’ll soon be able to design biocatalysts as good as natural ones, but for any problem we care about.
1. https://alexcarlin.bearblog.dev/novel-enzymes-from-a-diffusi...