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siminegroup / E2EDNA2

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Enhancement: Docking capabilities for atpamer and small-molecule interactions? #25

Open noah-camp opened 1 year ago

noah-camp commented 1 year ago

It seems that LightDock is capable of protein-protein, protein-peptide and protein-DNA docking. It is not suitable for small-molecule docking (in my case, I was interested in docking a DNA dopamine-specific aptamer with its ligand). It would be nice if there was a pipeline suitable for small-molecule docking; would this be out of the scope of this project?

Thank you!

InfluenceFunctional commented 1 year ago

@taoliu032 Can explain in more detail, but yes indeed we are aware of this capability gap and are working on an alternative for such situations.

taoliu032 commented 1 year ago

Hi @noah-camp, you are right about the limit. It was not our primary focus to develop a docking software that works for macromolecules and small molecules when we started the E2EDNA project, so we picked LightDock for its nice python API, as a proof of concept that any docker can in principle be integrated into the E2EDNA pipeline, with some necessary tweaks. You are more than welcome to try an alternative docker! And you can let us know here if you run into issues and need some help :)

A little bit of more detail: the module before the docking module spits out a PDB file to be docked with target molecule. So if you docker can take a PDB file, then it should only require a little effort.