Hello, I am a rookie in protein-small-molecule docking, I would appreciate it if you could give some suggestions.
I have read two publications about HADDOCK: (1) Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data (Structure, 2015); (2) Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing (J. Chem. Inf. Model, 2021).
And I was wondering if I could introduce the cryo-EM restraint of the small molecule when using HADDOCK to perform protein-small-molecule docking?
Similar work has been reported (GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps, Structure, 2020), and it was integrated into the Glide pipeline of Schrodinger software.
Thank you in advance!