- Some more evidence that BioEmu et al have largely rendered clever AF2 template and MSA hacks obsolete for quick conformational sampling of soluble monomeric proteins
- Accelerated sampling of protein dynamics using BioEmu augmented molecular simulation [new] BioEmu aids mol. simulation: capturing biomolecular dynamics (kinase transitions, mutation effects) via broader conformations.
- Personally skeptical of a paper making broad claims about such methods capturing mutation effects when their data is a single mutation in a single enzyme where effect is extensively studied & captured in many training data structures. AI structure/dynamics prediction tools are very poor VAEs imo
- Inverse folding much more promising bsky.app/profile/alic...
- Video introduction to our new “Conformational Biasing” method for computational design of mutations that bias proteins towards desired conformational states CB part starts at 14:55 Thanks to Peter Cavanagh and Andrew Xue – amazing graduate students who co-led this work
- I saw this, but this would only work if you were sure your reference distribution covered the full landscape right? It wouldn’t work for mutations that discover new states
- Yea this is not the same of course, but it just popped up in my feed and was close enough in topic ;) Still, there might be something there. Sample unbiased random flex and score with IF?
