Hi, I perform structure prediction for my designed vaccine construct using Robetta web server. And perform a validation score with PROCHECK to generate the Ramachandran plot and ERRAT scores. but the predicted structure for the designed protein does not achieved a good quality score for both ERRAT and Ramachandran. Any recommendations on how to improve the scores? Also, will the poor quality score of predicted structure protein affect protein-protein interactions?
Nur Arshad
It is a common issue while modeling a protein with minimal sequence similarity and coverage area. I suggest trying different ab-initio modeling servers like I-tasser to validate the model. If validated very well, but if not, then simulate your model under a force field parameter for a good time scale, and check for model accuracy using different validation parameters.
Thank you
Thank you so much for your recommendation. May I know, if the poor quality predicted structure of the protein will affect the folding and the binding interaction with other proteins during wet lab experiment?q
Nur Arshad
For sure,
the poorly modeled structure will have distorted folding and improper configuration of the secondary structured domain, which will show illogical interaction with other proteins upon docking.
The best is to go with MDS, for modeling as well as post-docking, to confirm your dock interactions between proteins.
Pawan Kumar Thank you so much for your reply.
I have done the MDS for my docked protein-protein complex using GROMACS following this tutorial http://www.mdtutorials.com/gmx/lysozyme/index.html. However, currently, I am having trouble to analyse the results from the simulation. I tried to use a tutorial from this YouTube video https://www.youtube.com/watch?v=thxwcKRolM4, changing all the selection options to protein instead of ligand, but my RMSD graph (attached) does not have a fluctuation plotting like in the video.
I think the plotted graph was based on the options I selected but I am able to figure out the solutions. Hoping anyone who is experienced with MDS in protein-protein complex can give some suggestions.
Thank you in advance.
Nur Arshad
Extend your simulation for a minimum of 20-50ns to check the behavior of protein structure when solvated in a water box.
Pawan Kumar do you know the approximate time taken for the simulation using a normal laptop?
The parameters for my previous simulation that I have done was dt = 0.001 and nsteps = 50000, and I think the process approximately took 8-12 hours. How do I estimate the time taken for the simulation of 20-50ns?
Nur Arshad
It depends on the hardware configuration of your laptop. The more graphic memory, it have, the quick the job will be done.
You can use command (gmx mdrun -v -deffnm md) to run md final run where -v will display the estimated time to complete the job.
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