please see the message, originally directed towards dr. sali, below.
if anyone has any comments, please send them!
many thanks,
doug kojetin
Begin forwarded message:
> Dr. Sali:
>
> I am a graduate student in the Department of Molecular and Structural
> Biochemistry at North Carolina State University. I have a question
> more about modeling process itself rather than the program MODELLER.
>
> I have used your program, MODELLER, to create models of a subfamily of
> proteins our lab and collaborators are interested in (total ~ 30).
> There are approximately 10 solved structures to the domain of
> interest. One of these solved structures (structure A) is in the same
> subfamily within the same species of proteins we are modeling (model
> A), whereas the other 29 proteins are of unknown solved structure. My
> question concerning the use of templates in the modeling process.
>
> ##############
> my main question
> ##############
>
> (if this is confusing, please let me know and i will rephrase) ...
>
> Would using a solved structure (structure A) to model a protein of
> exact sequence (model A) which will be used in a comparison of 29
> other structures with no known structures (and lower 'homology'
> compared to that of structure A to model A -- which is 100%) bias
> model A? Overall, we are interested in comparing all 30 structures.
> This comes mostly from outside comments that our modeled protein does
> not look 'exactly' like the solved structure. As one would like it to
> look as close as possible to the solved structure, it is a model after
> all, and perhaps we just need to be more descriptive in explaining our
> results, especially pertaining to this specific model.
>
> #####################
> how i modeled the proteins
> #####################
>
> I performed a 'modeling parameter assay' to find the number of
> templates to use to model a protein (model B), ranging from 1 to ~8
> templates. In addition, I 'assayed' the amount of refinement to use.
>
> Overall, I had an assay 'shaped' like a matrix with, for example,
> refinement across the top and # of templates going down. I produced 50
> models for each and ran a variety of analyses on the models (including
> Ca RMSD to the most homologous protein, ERRAT, PROCHECK, etc) and
> computed the average 'value' output from the respective analyses.
>
> All in all, using four (4) templates and a refinement value of 1
> produced the 'stereochemically best' models.
>
> I applied the same rationale to another protein of interest (model C),
> and the same trends were extrapolated.
>
> question
> --> is this rationale 'acceptable'? or how would you do something
> similar?
>
> Many thanks for your input, and I'm sorry for the long-winded email.
>
> Douglas Kojetin
