I have work with a protein and i made a homology model of the protein with swiss-model. I do all the thing which are required for docking then i only run the protein 100ns MD simulation. I got that result which i attached below. Now i am very eager to know if my protein is good or bad and the reason behind it. Thanks in advanced.
Visualize the trajectory to see how the system evolves in time. Plot backbone root-mean-square fluctuations to identify rigid and mobile regions. See what happens to RMSD plot if you align only the rigid core of the protein with the reference structure. Identify rigid-body (correlated) motions, which could be responsible for large RMSD fluctuations.
The rmsd plots alone are not reliable indicators of protein structure quality. Ramachandran plot is worth a try.
There are several aspects on determining the quality of a protein
1. After homology modelling, see the Ramachandran plot. There 2 things you have to observe. One is more than 90% residues of the protein must be within the favourable region and 2nd is the disallowed region. If you find some residues the disallowed region then at least give a try to eliminate that region via loop refinement. Several servers are present in this regard
2. ERRAT Score greater than 80%
If your protein follows this two criteria, then I think the quality of the protein is good.
RMSD value is required for docking and simulation purpose but for checking the quality of protein Ramachandran plot and different scores are important
Dear Ritwick Bhattacharya My protein fullfilled those 2 criteria but does not that type of RMSD value affect my docking?
would you like to tell me how i can get rid of these type of problem or how can i stable my protein?
If we consider you have done correct modelling, please share your mdp file to check what is going on.
Although your RMSD are really noisy, sometimes this is due to large unpacked loops. Since RMSD is a global index, you do not know the particular behaviour of the binding site. Try to follow RMSD only on your binding site or compare it with that of the scaffold for homology modelling. A recommendation is to use more than one snapshot of your MD and energy minimize them prior to docking.
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