Protein folding thread

[funkervogt]

Alphafold's error rate is higher than most people realize.

The estimate is that AlphaFold structures have somewhere between 7 and 20% of the side chain residues in an incorrect orientation - sometimes slightly off, sometimes way off. Those percentages seem to be the same for functional side chains as well as ones that are away from the action.

...That makes the current state of the art in protein structure prediction very useful as a hypothesis generator (and far beyond anything we had before), but it also means that, at least as we move into 2024, that it cannot replace experimental data, either. My own guess is that improvements in accuracy may turn out to be a sort of "last mile" problem that is unlikely to be solved by the sort of sudden advances that got us this far.

https://www.science.org/content/blog-po ... lace-world

[weatheriscool]

First synthetic protein motor creates its own fuel as it 'mows'
By Paul McClure
February 27, 2024
https://newatlas.com/science/synthetic- ... lawnmower/

The body uses protein-based molecular motors to perform functions essential to life. Now, researchers have created ‘The Lawnmower,’ the first synthetic motor modeled on those found in nature that propels itself by harnessing the energy it creates as it cuts through fields of proteins. It could transform our treatment of a range of diseases.

“Imagine if a Roomba could be powered only by the dirt it picks up,” said Nancy Forde, Simon Fraser University (SFU) physics professor and co-corresponding author of a study in which she and her fellow researchers outline their creation, a synthetic molecular motor that harnesses the energy of biological reactions to propel itself.

All living organisms, from humans to bacteria and plants, are kept alive by protein-based molecular motors that convert energy from one form into mechanical forces and motion that enable cell division, cargo delivery, movement towards food or light, and maintaining healthy tissues. SFU researchers, in collaboration with Lund University, Sweden, built on decades of research into the molecular motors seen in nature to realize their novel creation.