[Chimera-users] TM tendency hydrophobicity scale

[Shyam Saladi]

Hi,

I haven't fully formed an opinion yet. The methods in the paper sound
pretty interesting (not to mention the title), and it seems to be well
cited, too. It was also used in a recent paper
<https://www.ncbi.nlm.nih.gov/pubmed/29242231> on TA-protein targeting,
which had piqued my interest.

Thanks,
Shyam

On Fri, Feb 9, 2018 at 9:05 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Thanks, Shyam!
>
> If you have any comments about how the scales compare, I’d be interested
> to hear your opinion.  (If not, no problem… I can see you might be
> interested in trying it just from reading the paper.)
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Feb 8, 2018, at 6:26 PM, Shyam Saladi <saladi at caltech.edu> wrote:
> >
> > Hi all --
> > I have put together a Chimera attribute definitions to color residues
> according to the TM tendency hydrophobicity scale:
> >
> > Zhao and London, Protein Sci 15:8 (2006), doi: 10.1110/ps.062286306
> > An amino acid "transmembrane tendency" scale that approaches the
> > theoretical limit to accuracy for prediction of transmembrane helices:
> > relationship to biological hydrophobicity
> >
> > In case it's helpful to others, it's attached to this message. Perhaps
> the Chimera team would also be interested in including it with the other
> scales online as well.
> >
> > Thanks,
> > Shyam
>
>
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