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PostPosted: Fri Nov 13, 2015 10:11 am 
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Joined: Fri Nov 13, 2015 9:44 am
Posts: 5
Hi everyone,

currently I am design a virtual screening with AutoDock Vina.
I made several tests with a receptor and different ligands.
I came to the following conclusions:
- including flexible residues decreases (in average) the binding affinity of the highest ranking pose.
- The more flexible residues, the lower the best binding affinity.
- For small ligands the computation time is much lower without flexible receptor residues than with flexible residues.
- For large ligands the computation time is only slightly lower without flexible receptor residues than with flexible residues.

Did someone have similar experiences?

To me it seems therefore most favorable to use no flexible residues and therefore to use the saved computation time for more additional ligands, rather than the opposite way. Do you agree with that?

I look forward to hearing from you.

Best wishes,
Jadzia


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