Re: [phenixbb] alpha-Fold 2?

Depending on the target (i.e., free modeling, template based, etc.) the score follows a slightly different formula IIRC, but the major component is heavyatom GDT -- the assessors average the GDT evaluated with cutoffs at 1, 2, 4, and 8Å. I think it's 0-100 instead of 0-1 for reading ease more than anything else. On Mon, Nov 30, 2020 at 6:54 PM Aaron Oakley wrote:

Does “score" correlate with some estimate of the RMSD with respect to true structure?

–å

On 1 Dec 2020, at 7:22 am, Frank Von Delft wrote:

"Scores above 90 on the zero to 100 scale are considered on par with experimental methods, Moult says."

Who is it that does the considering for us? Great that it's good enough to make molecular replacement work (VERY great!!!!) - but "on par" is a big word.

Sent from tiny silly touch screen http://www.9folders.com/ ------------------------------ *From:* Jim Fairman *Sent:* Monday, 30 November 2020 19:58 *To:* lbetts0508 *Cc:* PHENIX user mailing list *Subject:* Re: [phenixbb] alpha-Fold 2?

For the most challenging proteins, AlphaFold scored a median of 87, 25 points above the next best predictions.* It even excelled at solving structures of proteins that sit wedged in cell membranes, which are central to many human diseases but notoriously difficult to solve with x-ray crystallography.* Venki Ramakrishnan, a structural biologist at the Medical Research Council Laboratory of Molecular Biology, calls the result “a stunning advance on the protein folding problem.”

Source: https://www.sciencemag.org/news/2020/11/game-has-changed-ai-triumphs-solving... -------------------------------------------------------------------------- Jim Fairman C: 1-240-479-6575

On Mon, Nov 30, 2020 at 10:25 AM lbetts0508 wrote:

...

all - I just read the blurb in Nature Briefing about the DeepMind AI having made a big advance in the CASP protein fold prediction.

Does it sound really transformational, does it work for membrane proteins - all the usual questions come to mind.

Do we know enough yet about it?

Signed an old protein crystallographer, L. Betts _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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