7 ms·
Yes: they predict structures using MSAs, without alignments to known protein structures in a majority of the cases.
by couteiral 5y ago
Yes: they predict structures using MSAs, without alignments to known protein structures in a majority of the cases.
- dekhn 5y agoOK if that's truly accurate, then they did make a significant accomplishment. However, I'm 99% certain (from reading the paper) that they actually do have alignments to structures, but the similarity is very low. It would help if you coould point to one of the alignmennts they made that has no underlying structure (even a template fragment) support. I reread the methods section, https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf https://static-content.springer.com/esm/art%3A10.1038%2Fs415... They train jointly on the results of genetic search and template search (template search). Can you show an example of a prediction made using only genetic search and not template search. Those templates are fastas made from PDB files, which, while not homology modelling, is definitely not "ab initio".
- dekhn 5y agoI've been in communication with several different teams and leaders at CASP and I've confirmed that this does appear to be the case. I'm going to be a bit skeptical but if that's the case, then it really is a significant improvement. Glad to see that with just the idea, the academic community was able to reach near parity in a short time, demonstrating there was nothing unique to DM except their huge amount of compute, storage, and talent, and this would have happened in the next CASP anyway.