Hi Reza, the term "validation" as used by e.g. crystallographers - namely by checking geometric parameters of a structure derived from experiment(s) - is euphemistic since realistic geometry is a required but not sufficient property of a model - it can be completely wrong even if it has good geometry. This type of validation should rather be called "checked for geometric consistency" or similar.
In general, the validation of a prediction should be performed by experiment(s). Ideally, that would be X-ray structure solution or cryo-EM or NMR. But it could also be e.g. a set of binding or cross-linking experiments, with suitable positive and negative controls. That a computational prediction can be "validated" by another calculation may be possible if the prediction is based on a set of facts that is disjoint from that of the "validation calculation". But this is not the case e.g. for models from AlphaFold or RoseTTaFold; MolProbility or similar programs could at most indicate that the prediction has failed, but not that the prediction is correct. Experiments are needed for this - and even these could be inconclusive. Best wishes, Kay On Mon, 20 Dec 2021 16:10:02 +0000, Reza Khayat <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 > >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/ > ######################################################################## 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/
