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

Dear Shruti,

Yes there is a problem with C- and TM-score of protein structure generated from I-tasser. But these problems can be overcome very easily. Have you done MD simulation of the protein structure alone before Autodocking ? If not, then re-perform MD simulation of the protein structure alone, extract average structure from stable plateau region. Validate the average structure using different online/offline tool, e.g. Ramachandran Plot and Z-score. Here you will observe better Ramachandran plot and Zscore, if you perform MD simulation in a correct way.

Additionally, collect information if your protein is a membrane or cytosolic protein while performing MD simulation because protocol/forcefield/parameters will change in both the cases.

Later go for autodocking and protein-ligand complex.

Hope this helps. If you want, you can follow these two paper :

Article In silico identification of natural product inhibitors for γ...

Best

Manoj

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

Could you please share the Ramachandran plot image and value before MD simulation. RMSD graph seems okay however there is a little scope for more simulation. But this should not be your concern right now. Try to extract average structure within 85 to 90 ns and re-do the validation. try to do comparisons between before and after simulation value and against different threshold parameters. If 90% of the parameters and value are corrects, I would suggest you can proceed with your analysis by explaining those 90% values in detail.

Thanks

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

Dear Shruti, I think you are not getting what I am trying to say :(

You have to compare Ramachandran plot value, Z score or any standard validation score of structure produced from I-Tasser ( Before simulation) as well as average structure produced after 100 ns MD simulation. At first see, if there is any change or not. If there is a changes, what are those changes.

Result which you are sending again and again is same data. So they are useless for comparative study

Please read literature I have asked you to read or any other standard literature of your choice. In my work I have explained about important parameter in detail

Hope this help

Best

Manoj

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.

Comparison between before and after MD will be great.