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) <https://www.iins.u-bordeaux.fr/> UMR5297 CNRS / UB Centre Broca Nouvelle-Aquitaine 146 rue Léo Saignat BP 61292 33076 Bordeaux Cedex <https://goo.gl/maps/CFNm4dUvzrmmHUM1A> France T: +33 (0)5 33 51 48 57 E: jonathan.eleghe...@u-bordeaux.fr W: https://www.iins.u-bordeaux.fr/ELEGHEERT Twitter: @ElegheertLab <https://twitter.com/ElegheertLab> ----------------------------------------------------------------- > On 8 Nov 2022, at 09:32, Jonas Emsley > <00008d0668c7d48d-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 <mailto:jonas.ems...@nottingham.ac.uk> > http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx > <image001.png>https://orcid.org/0000-0002-8949-8030 > > > > > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
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