[Chimera-users] Analysis of the multiple alignments + structures

James Starlight jmsstarlight at gmail.com
Thu Sep 4 00:14:49 PDT 2014

Elaine, thank you very much!

I'll try to check literature.



2014-09-03 19:36 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:

> Hi James,
> I’m glad you found a solution for the technical problem.
> I’m not really offering general research consulting on this list, and
> don’t claim to be an expert whose opinions should be followed.  That said,
> my general opinion is that evolutionary trace can offer additional insights
> to just looking at the conservation in the columns of one big alignment.
> Potential downsides are that for evolutionary trace you need a reliable
> phylogenetic tree, and to be careful about the range and balance of the
> data set of sequences.  In other words, tracing evolution is more difficult
> than just aligning the sequences, but then you can see correlations of
> specific mutations with evolutionary divergences.
> Rather than asking me, better to look in the literature.  I realize that
> is a daunting task, as there are many papers in this general area.  The
> Lichtarge group is continuing to explore evolutionary trace, and many other
> groups are using similar approaches.  My main involvement in the 2004
> Madabushi et al. paper was to compile the list of experimentally evaluated
> GPCR mutations and their literature references!
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 3, 2014, at 5:11 AM, James Starlight <jmsstarlight at gmail.com>
> wrote:
> > Thank you very much for suggestions!
> > Regarding techniqal question: Indeed I've found that the JalView +
> Chimera Mutalign give me best results! ;)
> >
> > Elaine, how do you think might the *selective* analysis of the
> alignments of *different* branches of the phylogenetic tree of the
> olfactory receptors be more effective for the the prediction of the
> mutations affecting its specifity and affinity towards different clases of
> ligands (odors)? I've noticed that the same aproach have been used in your
> 2003 study (Evolutionary trace of GPCRs) where you made conclusions (mainly
> based on the  selectivy analys of the Opsins) about mutations affecting i)
> ligand binding site, iii) constitutive activity as well as ii) coupling to
> the G-protein.
> >
> > Kind regards,
> >
> > James
> >
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