This sounds suspiciously like what the team from EBI that Eugene and I have
been working with either have done, or want to do.
They already have a way to cluster structures, but GESAMT is overfitting for
their needs. It might not for yours, but it would depend on exactly what you
want to do.
Where I've come in is in creating a program that can match and superpose
analogous chains from different structures and spit out progressively more
complete structures as more and more chains get matched and added. This assumes
there is high homology between structures, but it's not a requirement, though
its usefulness would decline as you move further away from homology.
The analysis would then be to try to figure out at what point do we say that
there has been a conformation change in the quaternary structure at the chain
level. I have some ideas, on how to accomplish this, but I'm still working on
parsing the output.
As far as having structures with wildly different homologies, I'd probably use
GESAMT, and try to figure out what parameters to use for clustering. Perhaps
the convex hull of the matched residues? Or even using SSM if there are
secondary structures and classifying them based on that? This paper I found
while researching the problem may give you some idea of how convex hulls could
be used to classify protein families.
@article{wang2007supervised,
title={Supervised classification of protein structures based on convex hull
representation},
author={Wang, Yong and Wu, Ling-Yun and Chen, Luonan and Zhang, Xiang-Sun},
journal={International Journal of Bioinformatics Research and Applications},
volume={3},
number={2},
pages={123--144},
year={2007},
publisher={Inderscience Publishers}
}
Sent from Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: Krissinel, Eugene (STFC,RAL,SC) <[email protected]>
Sent: Wednesday, March 8, 2023 12:54:07 PM
To: ccp4bb <[email protected]>; Eleanor Dodson <[email protected]>
Cc: Celis Garza, Daniel (STFC,RAL,SC) <[email protected]>
Subject: Re: [ccp4bb] Structural alignment and classification
yes selecting models and chains in SSM & Gesamt is possible -- Eugene
________________________________
From: CCP4 bulletin board <[email protected]> on behalf of Eleanor Dodson
<[email protected]>
Sent: 06 March 2023 14:55
To: ccp4bb <[email protected]>
Subject: Re: [ccp4bb] Structural alignment and classification
Does Superpose or GESAMT align multiple structures?
And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2
etc?
Eleanor
On Mon, 6 Mar 2023 at 14:53, Harry Powell
<[email protected]<mailto:[email protected]>>
wrote:
Or you could use Gesamt - also in CCP4.
Harry
> On 6 Mar 2023, at 13:15, Kay Diederichs
> <[email protected]<mailto:[email protected]>> wrote:
>
> Dear Armando,
>
> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign
> (https://zhanggroup.org/US-align/).
> In my tests, THESEUS sometimes crashed in different ways. USalign is very
> robust; SUPERPOSE is fast.
>
> HTH,
> Kay
>
> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert
> <[email protected]<mailto:[email protected]>> wrote:
>
>> Dear all,
>> I want to align several structures we obtained from a fragment screening
>> campaign and cluster them according to RMSD.
>> Is MNYFIT still running? What else can I run?
>> Thank you
>> Armando
>>
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