Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to
happen
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letin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eugene Valkov <eugene.val...@gmail.com>
Sent: Sunday, April 2, 2023 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to happen
Predicted
stru
ructures.
> That’s more damaging than helpful.
>
>
> --
> *From:* CCP4 bulletin board on behalf of Eugene
> Valkov
> *Sent:* Sunday, April 2, 2023 10:10 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] [External] Re: [ccp4bb] Structur
It has been mentioned that predictions might be misleading when it comes
to multi-domain complexes, probably due to the orientation of each
domain relative to the others rather than the fold of each domain
individually.
This is delicate since making a hypothesis based on inaccurate models
can
, 2023 10:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [External] Re: [ccp4bb] Structure prediction - waiting to
happen
Predicted structures lack the precision and accuracy of
experimentally-determined structures at high resolution with all the benefits
of unbiased co-discovery of
Predicted structures lack the precision and accuracy of
experimentally-determined structures at high resolution with all the
benefits of unbiased co-discovery of solvent molecules, ions, ligands,
etc., bound to molecules of interest.
It is also true that AI-assisted structure prediction can be stu
I am also not sure whether AlphaFold can address the impact of ions and other
cofactors on the fold of many proteins.
Best wishes,
Jacinto
On 2/4/23 16:20, Srivastava, Dhiraj wrote:
May be this article is of some help suggesting the need of
experimental structures despite excellent alphafold m
May be this article is of some help suggesting the need of experimental
structures despite excellent alphafold model.
https://www.nature.com/articles/s41401-022-00938-y
From: CCP4 bulletin board on behalf of Ian Tickle
Sent: Sunday, April 2, 2023 8:28 AM
To: CC
No offense to anyone but most of these systematic studies are often on small
not so flexible, single domain, easy to crystallize proteins with little
conformational variability and that’s where alpha fold excel. It fails with
(may not be all though) multidomain proteins with conformational varia
When I tested alpha fold on some of my proteins, it failed to predict the
intramolecular interactions needed for their functions. Alphafold predicts the
folds and overall structure of single domain and may be simple multi domain
proteins but when conformational changes are needed for protein fun
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