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
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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
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