Virtual screening by docking is very popular to identify novel ligands and there are a large number of tools that can be used “Autodock, Dock, FlexX, Autodock Vina, Fred, Haddock, Bude, Zdock, GOLD, Glide, FITTED, FlipDock, ADAM, MS-Dock, UCSF Dock, ParDock, FlipDock, PLANTS”.
Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.
A universal binary has just been made available https://sourceforge.net/projects/smina/files/smina.osx.12/download.
The ligandsForDocking.sdf file contained 1500 molecules as 3D structures. These were docked into a crystal structure of a kinase protein, with ligand bound, keeping the protein side-chains rigid.
Command used
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'/usr/local/smina.osx' --cpu 10 --seed 0 --autobox_ligand 'forDockingLigandOnly.pdb' -r 'forDockingNoLigand.pdb' -l 'ligandsForDocking.sdf' -o 'All_Docked.sdf.gz' |
The Intel MacBook Pro completed the task in 8 hours 30 mins and the fans came on after about 2 mins.
The MacBook Pro M1 max completed the task in 2 hours and 16 mins, the fans were silent.
List of tools tested https://macinchem.co.uk/software-reviews/cheminformatics-and-compchem-on-apple-silicon/
Last update 4 December 2021