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Method to capture receptor structure state after flexible docking #319
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Hi @eunos-1128 |
Both of them. Besides calculating them, I want to take closer look at differences among conformers using molecule viewer in detail. |
With Meeko v0.6 will be able to write a PDB of the entire protein with the updated positions of the sidechain. This is better for visualization and for integrating with other software, such as starting an MD simulation from docked poses. @eunos-1128 is this the feature/information you were looking for? |
@diogomart I'll try the script of meeko :) |
I could confirm sidechains in SDFs using
I want the structure of the entire protein right now. In Meeko's repo, there is a tag, called v0.6.0-alpha.3. I looked into the code but not sure of that. |
The alpha versions do not have that feature. Only v0.6 (non-alpha) will. The alpha were created to make some receptor preparation features more easily available before the a stable v0.6 is released. |
OK, Thank you. Until v0.6 is released, I'll manage with current version's meeko. |
Hi,
I'm interested in capturing the exact state of the receptor after flexible docking.
It seems there is no description about that on docs, but is there any way to do that with vina?
If not, does any other methods possible exist?
Regards,
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