Macs in Chemistry

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

The molecular operating environment MOE is an integrated molecular design and modelling platform that handles Small Molecules - Peptides - Biologics.

I'm very grateful for Chemical Computing Group for providing a M1 version of MOE and license key to test, and for the support providing helpful comments and suggestions.

Since I wanted to test the multiprocessor support I started MOE using on the M1 machine

$MOE/bin/moe -mpu 10

First read in 3g6d.pdb.gz this is virtually instantaneous on both systems.

Then run QuickPrep to prepare the structure

The Intel MacBook Pro took 1 minute 23 seconds
The M1 MacBook Pro took 41 seconds.

Then annotated (Antibody| IMGT), selected 3 residues as shown below and then ran a residue scan

proteinDesign

I took the average of 3 runs

The Intel MacBook Pro took 16 minutes 28 seconds
The M1 MacBook Pro took 6 minute 47 seconds.

Identical molecules SVL script

dbnbmols_incommon.svl calculates a matrix for the number of compounds each database has in common with each of the other databases based on either structure or fingerprints.

I used 26 databases of commercially available fragments that were loaded into individual MOE databases, the SVL script was then loaded and the command below used.

SVL command used

db_nb_mols_incommon [dbv_KeyList[], 'MatrixOut.txt', [write_cpds:1, cpds_outfile:'ident_cpds.txt']]

The Intel MacBook Pro took 6 minutes 35 seconds
The M1 MacBook Pro took 4 minute 14 seconds.

Importing files into MOE database

I imported a selection of structures from ChEMBL, 2D structures in sdf file format. MWt 250 to 500, calc LogP 0 to 5. This is a 2.6 GB file containing 1,144,624 molecules.

The Intel MacBook Pro took 13 mins
The M1 MacBook Pro took 5 mins

Processing sd FileČ™

MOE contains a collection of applications specially designed for processing structure data (SD) files from the shell command line.

sdwash applies washing rules and tautomer enumeration to structures in SD files. For testing I used a selection of structures from ChEMBL, 2D structures in sdf file format. MWt 250 to 500, calc LogP 0 to 5. This is a 2.6 GB file containing 1,144,624 molecules

Command used

time sdwash -pH 7 -salts ChEMBLsubset.sdf  -o output.sdf

The Intel MacBook Pro took 6 hours 11 mins
The M1 MacBook Pro took 3 hours 24 mins

Using moebatch

Pharmacophore searching is a critical part of virtual screening and is can be used to search very large datasets. Pharmacophore query generation in general requires user interaction and is not well-suited for batch mode. Pharmacophore search, on the other hand, can be done in MOE/batch using an SVL script or runnable file that invokes the SVL function ph4_Search. The search was run on a dataset of 274K structures using a predefined query. CCG also provided me with timings from other architectures and the results are shown below. As you can see the MacBook Pro M1 max out-performs all other platforms tested, this is particularly noticeable in the multicore performance, evaluating over 20,000 molecules per second. Whilst the fans came on after a minute or two with the other machines they remained silent on the MacBook Pro M1 max.

moebatch

List of tools tested https://www.macinchem.org/reviews/MacBooks/m1macbookpromax.php

Last update 21 December 2021