Dear Friends,
Welcome to the world of computational structure modeling. You can post all your queries regarding the topic.
I have modelled a structure for my protein sequence.Upon validation using PROCHECk, the ramachandran plot showed me a reliable value of 89.5%without energy minimization. Upon EM, it showed me 87.5%. My RMSD value was 0.07A degrees. Can I rely on the RMSD value and not energy minimization? suggestion pls.
Dear Nirmala, Let me know which tool you have considered for modelling and thereafter for EM?
Hello sir, I used swiss PDB viewer for modelling the protein sequence.
Dear Nirmala,
What you have used for energy minimization..same tool or something else?
If same tool i feel you better go with RMSD as the result is good.
The other option is use Modeller or as you are from VIT, I think you have INSIGHT or similar tool, that also you can look for.EM will be directly taken care off by this tools and you can choose your best model based on the DOPE score, Mod. Obj. Function etc.
Thank You, Sir for your suggestion. I used the same tool only for EM also sir.
I am in the starting stage of writing my first manuscript. Can you just provide some useful tips or advises to take care of in writing the same. How do I choose the journals for the publications?
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