Hi, I am a beginner in bioinformatics. I had determine the xyz coordinate of active site for my protein of interest, the coordinate was [69.37, 61.754, 58.738].
But when I repeat the same procedure on the same protein, the xyz coordinate has been changed to [ -9.604, 0.186, -20.754], does anyone know what happened and how to fix this?
This happened when I do docking with Autodock as well
Hi Sammy Zhen , can you elaborate more on how do you set up/input the coordinates on you protein and how did you save the coordinates? p/s: I'm more familiar with AutoDock
Hi Nor Farrah Wahidah Ridzwan , thanks for the reply. Actually I do not set up the coordinate. When I read the protein molecules and click on the grid box ( I choose center of the marcomolecule), the x,y,z coordinate changed. The changes was as mentioned in my question. I have re-downloaded the protein from the RCSB and the coordinate still show -ve values. I am sure whether I have clicked on anything accidentally, but would appreciate if your help and expertise in answering my question.
Thanks in advance.
Hi Sammy Zhen , I think the coordinate that you've obtained from journal is an altered coordinate. It means that, maybe the author moved the protein when viewing and saved it in a new coordinate. Thus, its center coordinate has been changed.
In my opinion, if you're doing specific docking, determine the active residues first and set up a grid box that can cover whole active residues.
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