[Chimera-users] TM tendency hydrophobicity scale

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 9 09:05:47 PST 2018


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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