[Chimera-users] Questions about probabilities in the Dunbrak library

[Elaine Meng]

Hi Tiglath, 
It is the probability given the phi and psi (backbone angles) of that residue, but that does not say anything about whether the rotamer sidechain fits well into your specific structure.  For example, .5 means that about 50% of residues of that same type (e.g. PHE) and that same backbone conformation have that sidechain rotamer, but in your specific structure, it might not fit (clashes) or some other rotamer might make better interactions (hbonds).  That's why the Rotamers tool also allows calculating hbonds and clashes, and why the "swapaa" command that mutates residues using rotamers does not use probability alone, instead it considers clashes (actually, fewer clashes better) and making good hbonds as more important than the probability value.

See "swapaa" option "criteria"
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria>

The Rotamers manual page 
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>

...gives the Dunbrack paper reference so you can see how they calculated the probabilities.
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Shapovalov MV, Dunbrack RL Jr. Structure. 2011 Jun 8;19(6):844-58.
<https://www.cell.com/structure/fulltext/S0969-2126(11)00144-4>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 31, 2021, at 3:57 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
> 
> Hi
> I'm trying to understand the meaning of probabilities in the Dunbrak library. From what I've found, this parameter is a measure of how probable a particular rotamer is to be found within a given conformation. Is this what this is?
> Thanks
> Tiglath