Hi, James, hi, everybody, somehow relevant to your, James, comments :
>>> MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5 >>> >>> I.E. What if we could train an AI to predict Rfree by looking at the >>> coordinates? if somebody missed, there is a couple of papers talking about a single / triple measure(s) of model quality : Shao et al ., 2017, Structure, 25, 458 Brzezinski et al ., 2020, The FEBS Journal, 287, 2685 Best regards, Sacha Urzhumtsev ----- Le 13 Jan 22, à 19:40, James Holton <jmhol...@lbl.gov> a écrit : > Agree with Pavel. > Something I think worth adding is a reminder that the MolProbity score only > looks at bad clashes, ramachandran and rotamer outliers. > MPscore=0.426∗ln(1+clashscore)+0.33∗ln(1+max(0,rota_out−1))+0.25∗ln(1+max(0,rama_iffy−2))+0.5 > It pays no attention whatsoever to twisted peptide bonds, C-beta deviations, > and, for that matter, bond lengths and bond angles. If you tweak your weights > right you can get excellent MP scores, but horrible "geometry" in the > traditional bonds-and-angles sense. The logic behind this kind of validation > is > that normally nonbonds and torsions are much softer than bond and angle > restraints and therefore fertile ground for detecting problems. Thus far, I am > not aware of any "Grand Unified Score" that combines all geometric > considerations, but perhaps it is time for one? > Tristan's trivial solution aside, it is actually very hard to make all the > "geometry" ideal for a real-world fold, and especially difficult to do without > also screwing up the agreement with density (R factor). I would argue that if > you don't have an R factor then you should get one, but I am interested in > opinions about alternatives. > I.E. What if we could train an AI to predict Rfree by looking at the > coordinates? > -James Holton > MAD Scientist > On 12/21/2021 9:25 AM, Pavel Afonine wrote: >> Hi Reza, >> If you think about it this way... Validation is making sure that the model >> makes >> sense, data make sense and model-to-data fit make sense, then the answer to >> your question is obvious: in your case you do not have experimental data (at >> least in a way we used to think of it) and so then of these three validation >> items you only have one, which, for example, means you don’t have to report >> things like R-factors or completeness in high-resolution shell. >> Really, the geometry of an alpha helix does not depend on how you determined >> it: >> using X-rays or cryo-EM or something else! So, most (if not all) model >> validation tools still apply. >> Pavel >> On Mon, Dec 20, 2021 at 8:10 AM Reza Khayat < [ mailto:rkha...@ccny.cuny.edu >> | >> rkha...@ccny.cuny.edu ] > wrote: >>> Hi, >>> Can anyone suggest how to validate a predicted structure? Something similar >>> to >>> wwPDB validation without the need for refinement statistics. I realize this >>> is >>> a strange question given that the geometry of the model is anticipated to be >>> fine if the structure was predicted by a server that minimizes the geometry >>> to >>> improve its statistics. Nonetheless, the journal has asked me for such a >>> report. Thanks. >>> Best wishes, >>> Reza >>> Reza Khayat, PhD >>> Associate Professor >>> City College of New York >>> Department of Chemistry and Biochemistry >>> New York, NY 10031 >>> To unsubscribe from the CCP4BB list, click the following link: >>> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] >> To unsubscribe from the CCP4BB list, click the following link: >> [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] > To unsubscribe from the CCP4BB list, click the following link: > [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
