<div dir="ltr">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.</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 30, 2020 at 6:54 PM Aaron Oakley <<a href="mailto:aarono@uow.edu.au">aarono@uow.edu.au</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Does “score" correlate with some estimate of the RMSD with respect to true structure?
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<div>On 1 Dec 2020, at 7:22 am, Frank Von Delft <<a href="mailto:frank.vondelft@cmd.ox.ac.uk" target="_blank">frank.vondelft@cmd.ox.ac.uk</a>> wrote:</div>
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<div id="gmail-m_1790925850024218106nine_body_n1761ad-0699f" dir="auto" style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;line-height:1.3;color:rgb(31,73,125)">
<div dir="auto">"<span style="color:rgb(51,51,51);background-color:rgb(255,255,255);font-weight:400;font-family:Roboto,"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px">Scores above 90 on the zero to 100 scale are considered on par with
experimental methods, Moult says."</span></div>
<div dir="auto"><span style="color:rgb(51,51,51);background-color:rgb(255,255,255);font-weight:400;font-family:Roboto,"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px"><br>
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<div dir="auto"><span style="color:rgb(51,51,51);background-color:rgb(255,255,255);font-weight:400;font-family:Roboto,"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px">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.</span></div>
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<div dir="auto">Sent from tiny silly touch screen<a href="http://www.9folders.com/" style="text-decoration:none;color:rgb(0,155,223)" target="_blank"></a></div>
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<div dir="auto" style="border:none;padding:3pt 0cm 0cm"><span style="font-size:11pt;font-family:Calibri,Arial,Helvetica,sans-serif"><b>From:</b> Jim Fairman <<a href="mailto:fairman.jim@gmail.com" target="_blank">fairman.jim@gmail.com</a>><br>
<b>Sent:</b> Monday, 30 November 2020 19:58<br>
<b>To:</b> lbetts0508<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] alpha-Fold 2?<br>
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<div><span style="color:rgb(51,51,51);font-family:Roboto,"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:16px">For the most challenging proteins, AlphaFold scored a median of 87, 25 points above the next best predictions.<b>
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.</b> 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.”</span> <br>
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Source: <a href="https://www.sciencemag.org/news/2020/11/game-has-changed-ai-triumphs-solving-protein-structures" target="_blank">
https://www.sciencemag.org/news/2020/11/game-has-changed-ai-triumphs-solving-protein-structures</a><br clear="all">
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<div>Jim Fairman</div>
<div dir="ltr"><span style="font-size:12.8px">C: 1-240-479-6575</span></div>
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<div dir="ltr" class="gmail_attr">On Mon, Nov 30, 2020 at 10:25 AM lbetts0508 <<a href="mailto:laurie.betts0508@gmail.com" target="_blank">laurie.betts0508@gmail.com</a>> wrote:<br>
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<div class="gmail_default" style="font-size:large">all - I just read the blurb in Nature Briefing about the DeepMind AI having made a big advance in the CASP protein fold prediction.</div>
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<div class="gmail_default" style="font-size:large">Does it sound really transformational, does it work for membrane proteins - all the usual questions come to mind.</div>
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<div class="gmail_default" style="font-size:large">Do we know enough yet about it? </div>
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<div class="gmail_default" style="font-size:large">Signed an old protein crystallographer, L. Betts</div>
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