click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
>
> --
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Pragu
epigenetic targets"
Department of Integrated structural biology
IGBMC,UMR7104 CNRS-UNISTRA, INSERM U 1258
phone : +33 (0)3 69 48 52 74
De: "Jan Dohnalek"
À: "ccp4bb"
Envoyé: Lundi 17 Janvier 2022 09:39:33
Objet: Re: [ccp4bb] Validation of structure prediction
I think
I think quite a bit of this "inconsistency" with protein structures comes
from the fact that with our larger globules it is much more true that our
model is an approximate time and space average of something that could have
the ideal geometry.
I.e. the way we are trying to represent the density is
On 1/13/2022 11:14 AM, Tristan Croll wrote:
(please don’t actually do this)
Too late! I've been doing that for years. What happens, of course, is
the "geometry" improves, but the R factors go through the roof. This I
expect comes as no surprise to anyone who has played with the "weight"
p
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
Hard but not impossible - even when you *are* fitting to low-res density. See
https://twitter.com/crolltristan/status/1381258326223290373?s=21 for example -
no Ramachandran outliers, 1.3% sidechain outliers, clashscore of 2... yet
multiple regions out of register by anywhere up to 15 residues! I
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 pept
Hi,
try SAVES online tool,and ProSa.
On Mon, 20 Dec, 2021, 9:40 pm Reza Khayat, 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
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
t
n behalf of Krieger,
> James M
> *Sent:* Tuesday, December 21, 2021 7:14 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [EXTERNAL] Re: [ccp4bb] Validation of structure prediction
>
> There are also dedicated homology modelling validation tools such as
> ANOLEA (ANOLEA (Atomic Non-Lo
York, NY 10031
From: CCP4 bulletin board on behalf of Krieger, James M
Sent: Tuesday, December 21, 2021 7:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] Validation of structure prediction
There are also dedicated homology modelling validation tools such as ANOLEA
(ANOLEA (A
] Fwd: [ccp4bb] Validation of structure prediction
Dear all,
this is by far not the general case in our hands. Depending on which AlphaFold
protocol is used, the resulting models have locally disfavourable
geometries–including clashes–, impossible chain crossovers, etc. I would
definitively
uesday, December 21, 2021 11:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Validation of structure prediction
Reza,
Thus far, it seems we’ve all assumed this was an AlphaFold or RobettaFold
model. If this is not indeed the case, it may be worthwhile to “validate” your
mode by runnin
Reza,
Thus far, it seems we’ve all assumed this was an AlphaFold or RobettaFold
model. If this is not indeed the case, it may be worthwhile to “validate”
your mode by running your sequence through one of these two and using the
validation from them.
The AlphaFold DB can be found here, with a numb
Just to add one point that I don’t think I’ve seen yet. If what the referee
wants is a data-free assessment of the expected quality of the model, I think
that the best assessment at the moment is the one done by AlphaFold2 (or indeed
RoseTTAFold if you’re using one of their models). The machine-
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 ge
04
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction
Dear all,
this is by far not the general case in our hands. Depending on which AlphaFold
protocol is used, the resulting models have locally disfavourable
geometries–including clashes–, impossible chain crossovers,
u know support each other.
Cheers
M
*From:* CCP4 bulletin board on behalf of Tristan
Croll
*Sent:* 21 December 2021 08:28
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Validation of structure prediction
I agree wit
the structure and see
if the atom positions and what you know support each other.
Cheers
M
From: CCP4 bulletin board on behalf of Tristan Croll
Sent: 21 December 2021 08:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Validation of structure prediction
I
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 pr
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
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
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