Re: [ccp4bb] Optimising a Nanobody interface computationally to improve binding

[Jonathan Elegheert]

Hello,

Indeed, Rosetta-ddG can evaluate the effect of residue mutations. Also, have a 
look at the program FoldX for per-residue evaluation of mutations 
(https://foldxsuite.crg.eu/). Then, there is the freeware webtool FireProt, its 
algorithm uses FoldX as a pre-filter to select beneficial mutations which are 
subsequently proved in a second round using Rosetta-ddG 
(https://loschmidt.chemi.muni.cz/fireprotweb/).

Overall my understanding is that these programs evaluate destabilising 
mutations more accurately than stabilising / affinity-enhancing mutations … but 
it may give interesting leads.

Cheers
Jonathan

-
Jonathan Elegheert, PhD
Team Leader
CNRS Scientist

Interdisciplinary Institute for NeuroScience (IINS) 

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E: jonathan.eleghe...@u-bordeaux.fr
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Twitter: @ElegheertLab 
-






> On 8 Nov 2022, at 09:32, Jonas Emsley 
> <8d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
>  
>  
> Dear all
>  
> I have a protein engineering question.
>  
> If you have a nanobody ligand complex structure is there a program that can 
> use the crystal structure to suggest engineering  improvements to give a 
> tighter binding nanobody. It need not just be in the CDRs. Maybe rosetta can 
> do this? 
>  
> Any suggestions will be greatly welcome
>  
> cheers
>  
> jonas
>  
>  
>  
>  
> ##
> Dr Jonas Emsley
> Professor of Macromolecular Crystallography,
> Nottingham Biodiscovery Institute 
> School of Pharmacy,
> University of Nottingham,
> University Park,
> Nottingham.
> NG72RD
> Tel: +44 1158467092
> Fax: +44 1158468002
> email:jonas.ems...@nottingham.ac.uk 
> http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
> https://orcid.org/-0002-8949-8030
>  
>  
>  
>  
>  
>  
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[ccp4bb] Optimising a Nanobody interface computationally to improve binding

[Jonas Emsley]

Dear all

I have a protein engineering question.

If you have a nanobody ligand complex structure is there a program that can use 
the crystal structure to suggest engineering  improvements to give a tighter 
binding nanobody. It need not just be in the CDRs. Maybe rosetta can do this?

Any suggestions will be greatly welcome

cheers

jonas




##
Dr Jonas Emsley
Professor of Macromolecular Crystallography,
Nottingham Biodiscovery Institute
School of Pharmacy,
University of Nottingham,
University Park,
Nottingham.
NG72RD
Tel: +44 1158467092
Fax: +44 1158468002
email:jonas.ems...@nottingham.ac.uk
http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx
[ORCID iD icon]https://orcid.org/-0002-8949-8030









This message and any attachment are intended solely for the addressee
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