Hello everyone,
I used Cluspro to dock my protein of interest with several kinase proteins. Then, I analyzed the results using PDBsum and ProQ. I have a question regarding the ProQ results. For all my docked models, the Predicted LGscore was higher than 5, but the Predicted MaxSub was approximately -0.5. I'm not sure how to interpret this and whether I can consider my docked models acceptable or not. It's worth mentioning that I docked the entire protein, not just a short sequence, which may explain the negative value of MaxSub, is not it? Additionally, 79 to 85% of the protein residues in my models fall in the Most favored regions according to the Ramachandran Plot statistics, and the G factors range between -0.4 to -0.54. So, could someone please explain if my models are acceptable based on these statistics?
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