As for the approximation of the on-rates being the same, this could be a
requirement to avoid over-fitting. You should look that up. Does the Li et
al. paper make similar assumptions? The problem with the 3+ site models is
that there are often too many parameters and the optimised result is complete
nonsense that has absolutely nothing to do with reality. So you have to make
assumptions to create a parametrised model that will give a result grounded in
reality.
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**[tickets-support:#4] 4-State ligand binding - relaxation dispersion analysis**
**Status:** open
**Release:** 4.2
**Created:** Wed Feb 19, 2025 05:54 PM UTC by Ana Clara Granja
**Last Updated:** Thu Feb 20, 2025 08:24 AM UTC
**Owner:** nobody
Hello,
I have a set of concentration-dependent 1H-RD-CPMG experiments, with one CPMG
experiment conducted for each concentration of the ligand. I am interested in
globally fitting a 4-state ligand binding model, where conformational selection
and induced fit are interconnected in a cycle, to the relaxation dispersion
curves using the Bloch–McConnell equation in order to determine the kinetic
constants of the model.
Would it be possible to implement a routine to perform this type of analysis in
relax?
For reference for the type of analysis I'm trying to do is described here:
https://doi.org/10.1073/pnas.2317747121 . In this study, use an approximation
assuming that the on-rate constants of the two pathways are identical. However,
since this is not a general case, it would be ideal to work with the model
without applying this approximation.
Additionally, they use grid search strategy to improve initial value selection
to the fitting, it would be very helpful if this could also be implemented.
Thank you in advance for your time and consideration.
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