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

James Starlight jmsstarlight at gmail.com
Mon Sep 1 02:55:50 PDT 2014


I have not fully finished your tutorial but now I have one question: have
you seen some intresting papers covering my problem: to make prediction of
the functional properties of some amino acid (motifs) based on the analysis
of the 3D structure of the protein under interest together with the
analysis of sequences of closely related homologues?

In particular I'm interested of how much sequences should I include to the
MSA and what threshold for the seq identity (agains my target protein)
should be chosen. E.g In case where I deal with the set of G-protein
coupled receptors (which has low sequence similarity but hight structure
conservation): I've obtained 2 different pictures of the conservative a.a
motifs in cases where i've used i) only several templates with low sequence
(40%) identity VS ii) where I have used alot of sequenses with begger
identity (up to 60%). In the latter cases I've obtained much bigger
conservation in the motifs seen based on the analysis of SS( which is
trivial!) where in the i) case- there were only several highly conservative
motifs. Does it means that the analysis of BIG datasets with bigger
sequence identity produce bigger unsertaintly in the final results because
we can conclude about what conservative elements are *really* functional


2014-09-01 11:36 GMT+04:00 James Starlight <jmsstarlight at gmail.com>:

> Thanks alot!!
> James
> 2014-08-29 19:43 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:
> Hi James,
>> These tutorials may also be worth a look, or at least a glance to see if
>> they cover things you want to know about:
>> Structure Analysis and Comparison
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
>> >
>> Functional Annotation Scenario: The Structure-Function Linkage Database
>> (SFLD) and Chimera
>> <http://www.rbvi.ucsf.edu/chimera/data/sfld2014/sfld2014.html>
>> Elaine
>> On Aug 29, 2014, at 10:23 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> > Hi James,
>> > It happens that I just finished making a new online tutorial “mapping
>> sequence conservation onto structures with Chimera”!!
>> >
>> > <http://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>
>> >
>> > The tutorial has  lots of links and details.  I’m not aware of plugins,
>> but Chimera’s Multalign Viewer is very rich in features for this type of
>> work; it includes a variety of options for calculating and displaying
>> conservation, mostly provided via the included AL2CO program from the
>> Grishin group. Anyway, that and much more is described in the new tutorial
>> and links therein.
>> >
>> > Some of the tutorials in the User’s Guide (included with Chimera
>> download) also address this area, with a bit less detail:
>> >
>> > Sequences and Structures: <
>> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
>> > Superpositions and Alignments: <
>> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html
>> >
>> >
>> > Of course, besides the sequence-related features, you could still use
>> general structure analysis (H-bonds, Rotamers, etc.) to investigate your
>> sequence-structure hypotheses.
>> > I hope this helps,
>> > 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 Aug 29, 2014, at 3:52 AM, James Starlight <jmsstarlight at gmail.com>
>> wrote:
>> >
>> >> Dear Chimera Users!
>> >> I'd like to perform analysis of the set of the sequences (presented in
>> the FASTA multiple-alignment file) together with the some (not all) X-ray
>> structures available for several of the sequences presented in its database
>> to detect conservative motifs (from sequence) and make conclusions about
>> its functional importance (based on the analysis of the Xray data) to make
>> conclusions between conservation of sequence and it's functional relevance.
>> Could you provide me with the some useful Chimera plugging as well as for
>> some tutorials
>> >> Kind regards,
>> >> James
>> >
>> >
>> > _______________________________________________
>> > Chimera-users mailing list
>> > Chimera-users at cgl.ucsf.edu
>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> >
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