Sam Berry
@sberry.bsky.social
Harvard Biophysics PhD candidate studying protein evolution with a focus on transporters in the Gaudet and Marks labs. Occasional fiction writer. Proud cat dad.
Yes, I think I agree. There are two problems: 1) the approach they use isn’t very accurate even for natural proteins and 2) any model will behave very differently for sequences close to the training set than for those far away, so their result is expected just from how the model is trained
September 1, 2025 at 4:58 PM
Yes, I think I agree. There are two problems: 1) the approach they use isn’t very accurate even for natural proteins and 2) any model will behave very differently for sequences close to the training set than for those far away, so their result is expected just from how the model is trained
To my knowledge there is no evidence that that networks like ESMFold accurately predict structural perturbations upon mutation? So yeah seems it’s entirely analysis *of the model* not of actual protein biophysics
September 1, 2025 at 1:08 PM
To my knowledge there is no evidence that that networks like ESMFold accurately predict structural perturbations upon mutation? So yeah seems it’s entirely analysis *of the model* not of actual protein biophysics
Reposted by Sam Berry
RFK Jr. is not a vaccine skeptic. He's a vaccine denier whose anti-science extremist views and actions are destroying one of humanity's greatest scientific achievements. He's going to kill a lot of people, and those deaths are on the 52 Republican senators who confirmed him and those enabling him.
August 31, 2025 at 7:45 PM
RFK Jr. is not a vaccine skeptic. He's a vaccine denier whose anti-science extremist views and actions are destroying one of humanity's greatest scientific achievements. He's going to kill a lot of people, and those deaths are on the 52 Republican senators who confirmed him and those enabling him.
As a note - AlphaFold and other similar algorithms can still do reasonably well without MSA info. They really have learned principles from the PDB (but these principles are NOT physical protein folding - as evidenced by that they can’t predict destabilizing muts etc)
June 5, 2025 at 12:36 PM
As a note - AlphaFold and other similar algorithms can still do reasonably well without MSA info. They really have learned principles from the PDB (but these principles are NOT physical protein folding - as evidenced by that they can’t predict destabilizing muts etc)
Thanks, will check these out!
May 4, 2025 at 6:31 PM
Thanks, will check these out!
Do you think it would be be more reasonable to benchmark these kinds of models against raw NMR data (e.g. by simulating NMR data from the predicted ensemble, if that’s possible) or are there still too many sources of variability going into the raw data?
May 4, 2025 at 6:09 PM
Do you think it would be be more reasonable to benchmark these kinds of models against raw NMR data (e.g. by simulating NMR data from the predicted ensemble, if that’s possible) or are there still too many sources of variability going into the raw data?