Elaine,

I completely agree with you. Iam trying to make some presentation for nonscientific folks, hence the query.

Thanks

Krish

 

Sent from Mail for Windows

 

 

[EXTERNAL]

Hi Krish,
It is rarely possible to show some kind of obvious visual/structural correlate to energy improvements of a kcal or two from a simplistic approach to virtual mutation such as the sidechain swaps that ChimeraX does.  One might need to do a full-scale new prediction of the  mutant structure in some other program, or even do a long dynamics simulation (or free energy perturbation simulation with gradual mutation) to gain insights into the contributions to the change in affinity.  It might be something quite subtle like changing the conformational entropy of the unbound state.

Just my two cents'
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Jul 24, 2023, at 10:12 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> From: Krishnan Raman <RKrishnan@BIOCRYST.com>
> Subject: depicting contacts
> Date: July 24, 2023 at 9:50:11 AM PDT
>
> Hi all,
> Any ideas to depict a dramatic improvement(200 nm to femtomolar) in binding affinities  before and after mutations(about seven) in chimerax?
> II have tried contacts , swapaa etc. nothing seems dramatic enough for visuals
> Thanks
>