Hi,

I would suggest you to consider energy minimization of your protein, you can submit it to CABS Flex server or use MDWeb server for this purpose. CABS Flex will be easier to use. Once again perform structural validation post simulation. Proceed with the best structure after that. Hope this helps.

Best Wishes

Pankaj

Thanks Manoj for you reponse. I have performed MD simulation of predicted protein model RMSD trajec. of the same i have attached in word file. Please have a look.

Thanks

Thanks

Ramachandran plot that I have attached is of before MD simulation.

Okay sorry.

I have gone through your paper . You have explained very well. I got my answer.

Thank you very much.

As Manoj Kumar Gupta said take the best stable structure after MD, then do the structure validations and compare the validation results with your modeled protein. This is the best idea to proceed further with your protein.

In other hand, you can try different modelling servers like Robetta or other softwares.