I had predicted 3D structure of protein using I-TASSER as there are no template that satisfied match with the protein sequence. Then I checked the Ramachandran plot to determine the reliability of the prediction. 70% protein residues are inside in allowed region. Then I proceed with loop refinement (15 loops). After that, the value is increased to 82%. Is it I need to increase again the value? Another thing, is it I need to do MD after that? What is the purpose to do MD? Is it to see the stability of the protein or to know the most stable conformation of protein? What is the parameter that I can use as a start to run MD as there are no reference? How to know if the protein is unstable because of the condition of MD is unfavorable or the protein conformation is not good?
Depending on available compute resources, instead of running MD simulation, you may use some structure refinement tool (GOAP, ModRefine, GalaxyRefine, etc.) as it would be more time and compute efficient. Also, to assess the reliability of predicted model structure, I would suggest you implement some more comprehensive approach instead of considering Ramachandran allowed region solely (ProTSAV, SAVES, etc.).
Please follow the above said answers for protein structure refinement and dynamics. MD is a essential method to validate your model protein is a stable structure for proceeding further analysis in CADD (i.e Molecular docking or complex dynamics).
The MD will provide the following supportive data
1. Stability of the protein structure
2. RMSD in angstrom (Helpful to find the stable conformation structure and equilibrated state of your protein)
3. How it behaves in the solvent environment (Pressure+Temperature).
4. Individual atomic motions as a function of time.
Please refer the following article, it may be useful to know better
Article Assessment of ab initio models of protein complexes by molec...
https://www.pnas.org/content/102/19/6679
Good Luck.
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