lysozyme (u/lysozyme)

lysozyme commented on Egypt declared malaria-free after 100-year effort bbc.com/news/articles/cm2... · Posted by u/thunderbong

lysozyme · a year 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...

lysozyme commented on Chemistry Nobel: Computational protein design and protein structure prediction nobelprize.org/prizes/che... · Posted by u/mitchbob

lysozyme · a year 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...

lysozyme commented on Apple Watch Series 10 apple.com/newsroom/2024/0... · Posted by u/latexr

rtpg · a year ago

I used to use smartwatch timers a lot. I bought a couple magnet timers to throw onto my fridge instead. Best $3 purchase I've ever made. Just smash the buttons, hit it, and go about your day.

lysozyme · a year 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

lysozyme commented on AlphaProteo generates novel proteins for biology and health research deepmind.google/discover/... · Posted by u/meetpateltech

flobosg · a year ago

In my humble opinion, this work is not that innovative: de novo protein binders have been done to death, either by AI approaches or otherwise. Check out the work by David Baker’s group, for instance. They have a myriad of examples already.

That being said, as others have commented, my hopes are that all these advancements lead finally to reliable design methods for novel biocatalysts, an area that has been stalling for decades, compared to protein folds and binders.

lysozyme · a year 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...