Dear Reza,
You may run it through the Moleprobity server for validation:
http://molprobity.manchester.ac.uk/
Good luck, Anat.
From: CCP4 bulletin board On Behalf Of Reza Khayat
Sent: Monday, 20 December 2021 18:10
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4bb] Validation of structure prediction
Dear all
I have a new studentship open, "Fragment to Field", to work on the
details of how to use fragment approaches for crop science.
Please circulate to any students you're aware are interested in this
kind of thing.
Webpage is here:
https://www.ndm.ox.ac.uk/study/dphil-themes?project=
Prof. Alfredo Torres-Larios (1973-2021).
It is with great sadness and with a heavy heart that this email is to notify
the scientific community of Crystallography about the tragic passing of Prof.
Alfredo Torres-Larios this past September 9th, 2021, in Mexico City, at the
early age of 48.
.-
His
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
The Molprobity server can be run online and only requires the coordinates
in PDB format: http://molprobity.biochem.duke.edu/.
Best,
Nick Clark
On Mon, Dec 20, 2021 at 11:10 AM Reza Khayat wrote:
> Hi,
>
>
> Can anyone suggest how to validate a predicted structure? Something
> similar to wwPDB
Hello,
another one . http://bioinfo.ifm.liu.se/ProQ2/
Best regards
Jeroen
Am 20.12.21 um 17:39 schrieb Weidenhausen, Jonas:
Hi Reza,
Could you use MolProbity (also from within Phenix), which will give
you statistics about Ramachandran/rotamer outliers, clash score etc?
Besides, maybe M
Hi Reza,
Could you use MolProbity (also from within Phenix), which will give you
statistics about Ramachandran/rotamer outliers, clash score etc?
Besides, maybe ModFOLD? (https://www.reading.ac.uk/bioinf/ModFOLD/)
Which journal, if I may ask?
Best,
Jonas
--
Jonas Weidenhausen
PhD Student
AG Sin
?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 mi
Dear Member of the CCP4 Community,
Would you describe yourself (or someone you know*) as a Masters or PhD student, or an Early Career Researcher (i.e. with up to 5 years post doctoral experience at 11th March 2022)?
If so, you could be eligible to appl
