I agree with Dale. Tools like MolProbity are not the right approach to validating a structure prediction. To understand why, just consider that all you need to do to get a perfect MolProbity score is predict every structure as a single long alpha helix with ideal rotamers, with a kink at each proline.
To validate a predicted structure will require a completely different toolset - one that I’m not sure fully exists yet. — Tristan > On 20 Dec 2021, at 18:47, Dale Tronrud <de...@daletronrud.com> wrote: > > I don't see any reason to believe that software designed to validate > crystallographic or NMR models would have any utility validating AlphaFold > predicted models. Doesn't the prediction software already ensure that all > the indicators used by Molprobity are obeyed? I'm afraid that the tools to > validate any new technique must be designed specifically for that technique. > (And when they become available they will be useless for validating > crystallographic models!) > > Dale E. Tronrud > >> On 12/20/2021 10:28 AM, Nicholas Clark wrote: >> The Molprobity server can be run online and only requires the coordinates in >> PDB format: http://molprobity.biochem.duke.edu/ >> <http://molprobity.biochem.duke.edu/>. >> Best, >> Nick Clark >> On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat <rkha...@ccny.cuny.edu >> <mailto: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> >> -- >> Nicholas D. Clark >> PhD Candidate >> Malkowski Lab >> University at Buffalo >> Department of Structural Biology >> Jacob's School of Medicine & Biomedical Sciences >> 955 Main Street, RM 5130 >> Buffalo, NY 14203 >> Cell: 716-830-1908 >> ------------------------------------------------------------------------ >> 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/ ######################################################################## 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/
