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bioexcel / biobb_chemistry

Biobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
https://mmb.irbbarcelona.org/biobb/
Apache License 2.0
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Include faster options to generate 3D coordinates with OpenBabel for larger virtual screenings #5

Closed PabloNA97 closed 1 year ago

PabloNA97 commented 1 year ago

I think the current approach is to include the --gen3d flag to generate the minimum energy conformer for a given ligand. It would be very interesting to have access to other faster options as described in the Open Babel manual, specially in the context of a large virtual screening.

I don't have a lot of experience on this so correct me if I'm wrong. But I would imagine that the conformational exploration done by AutoDock Vina on the ligand makes the search for the lowest energy conformer before the docking a bit redundant and undesirable to screen very large libraries.

Thank you! :)

gbayarri commented 1 year ago

Hi @PabloNA97 ,

Feel free to open a new PR with the desired flags for the obabel tools.

Best.

github-actions[bot] commented 1 year ago

This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed.

github-actions[bot] commented 1 year ago

This issue was closed because it has been inactive for 14 days since being marked as stale.