protein structure modeling

Question

[Shamim Sarhadi]

Hi I am new in protein modeling and I want to model a protein, my protein has 2 fragments, one of them related to functional domain and the other is a ten aa fragment that binds to receptor, I searched here for the posts about best tools and tutorials, but those back to years ago, please tell me about the best and user-friendly tools

[Nestor Wendt]

SWISS-MODEL is good and user-friendly.

[Shamim Sarhadi]

I have tried with swiss-model but one fragment of my protein in the searching step for template did not have any result, I think this lead to decrease in accuracy of the model

Answer 1

[Ibrahim Tanyalcin]

Dear Shamim,

There are a couple of stand alone or online versions when it comes to modeling. For instance there is modeller, I-TASSER, phyre 2, FoldX etc. They more or less combine homology modeling for regions where there is a similar structure in their database and ab initio modeling (from scratch using simulations) for regions where there is no known homologous structure. The results are somewhat ambiguous. To assess the accuracy of models that are predicted, programs compete every now and then in The Critical Assessment of protein Structure Prediction (CASP) competition. There, you can check which performs best in every year.

One thing I should underline though, is that you have to be careful if the program you use does not totally engage in changing the alpha carbon backbone of your protein. This means that only local energy minima will be satisfied and your overall structure may very well not reflect reality at all. This also means that energy minimizations alone will not help you obtain a realistic model. I would combine several tools and compare the results rather than going for the "best tools".

Regards,

[Shamim Sarhadi]

Thank you for your helpful advice Ibrahim Tanyalcin

I think the biostar site already has a vote button, to thank someone but I can't see that, does it change?

all the best

[Ibrahim Tanyalcin]

If the answer is helpful and you say it is than it is the best acknowledgement. No worries man,:) Good luck with your modeling.