Macs in Chemistry

Insanely great science


Comparing SMINA on a M1 MacBook Pro Max with Intel MacBookPro (2016)

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

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

'/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

Last update 4 December 2021