please help me I am working on mutate and normal protein in comparison. I do docking of both proteins with compounds. The compound shows binding to phosphate of mutated structure and the same compound show no binding with the phosphate of normal structure. How can i justify my results through literature? Is these results are good or not?
Phosphate was already present in the receptor? is that what you are trying to say? or the ligand having the phosphate group is interacting with the receptor?
Considering that the phosphate group of ligand is interacting with the receptor, in order to compare the results you need to see glide scores, MMGBSA scores or docking scores.Say for example if mutated protein-ligand complex has better MMGBSA score then, you can say that theoretically the binding affinity of x ligand is better in the mutated protein.
there are many question which you need to keep in mind to justify or elaborate your result
1. why you dock the ligand in the enzyme receptor?
2. Did you do point/multiple mutation in the active region or somewhere?
3. Did you want to find the binding afinity of both type of enzyme?
Abdul Nasir yes multiple mutation were done in the structure. I dock the ligand in the enzyme receptor to inhibit the over expression of this enzyme. yes want to find binding affinity of both type of enzyme i am caring a comparative study of both normal and mutated enzyme
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