I had finished docking with MOE molecular operating environment, However, I was faced with docking result, what this result and how to find the affinity, binding and number, and type of binding?
Hi,
the simplest way is for you to only consider the final score ("S"), as it involves all other terms. You can get more information on the MOE Help Topics.
Hi Hany,
The most straightforward way is to compile the data based on the "S" score table and as you can see it is in descending order, the more negative the better. Hence you can use the top 5-10 from the table you have in MOE to show best poses.
Just a small addition, try to use induced Fit and not rigid receptor as I have always found the former to work more accurately and give you a better docked pose.
Please feel free to post more questions if you have.
Hi,
As mentioned in previous answers, you can just consider the score (S). and to visualize the 2D- interactions, you can use ligand interaction option while browsing your results.
Also, you can change the scoring functions to get better more representative results, assessed by validation and redocking of the co-crystalized ligand (if present).
In the docked database (MDB), Select Compute => Descriptors => Calculate ... and then calculate which factor you want to do.
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