3 ms·
Same as any other prediction I'd presume. Run it against a known protein and see how the answer lines up. Predict the structure of an unknown protein, then us
by luma 4y ago
Same as any other prediction I'd presume. Run it against a known protein and see how the answer lines up. Predict the structure of an unknown protein, then use traditional methods (x-ray crystallography, maybe STEM, etc) to verify.
- christudor 4y agoThis is exactly right.
- gilleain 4y agoAs a simple example, one measure used to compare a predicted structure against a reference is the RMSD (root mean square deviation). https://en.m.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions https://en.m.wikipedia.org/wiki/Root-mean-square_deviation_o... The lower the RMSD between two structures, the better (up to some limit).
- iandanforth 4y ago"Verify" is almost correct. The crystallography data is taken to be "ground truth" and the predicted protein structure from AlphaFold is taken to be a good guess starting point. Then other software can produce a model that is a best fit to the ground truth data starting from the good guess. So even if the guess is wrong in detail it's still useful to reduce the search space.