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modeling question



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
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(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.

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how i modeled the proteins
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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