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 <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> online as well. Thanks, Shyam -- Shyam Saladi <http://shyam.saladi.org> NSF Graduate Research Fellow Biochemistry and Molecular Biophysics California Institute of Technology
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@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
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@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@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
Hi Shyam, After skim-reading the paper and trying the “TM tendency” scale on a few different structures, it seemed worthwhile to add. I was interested in trying it myself. :-) Additions are in the “hydrophobicity” page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> … and the list of example attribute-definition files: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#examples> Let me know if there’s anything about the credit to you that you’d like changed. I included a middle initial for specificity, not knowing if there are other people with your same name. Thanks for the contribution! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2018, at 11:45 AM, Shyam Saladi <saladi@caltech.edu> wrote:
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 on TA-protein targeting, which had piqued my interest. Thanks, Shyam
On Fri, Feb 9, 2018 at 9:05 AM, Elaine Meng <meng@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@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
participants (2)
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Elaine Meng -
Shyam Saladi