Elaine,

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 importnat?

James

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

Thanks alot!!

James

2014-08-29 19:43 GMT+02:00 Elaine Meng <meng@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@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@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
>
>

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