Shape based molecular screening using GPU
This tutorial will show how to use the Schrödinger Maestro Shape tool to quickly screen the Molport molecular database with 16 million structures (160 million conformations) on a GPU in Puhti.
Preparing the Molport database for GPU screening takes two weeks, but since the prepared shape file is already available on Puhti the actual screening of your molecule takes only 5-20 minutes on a GPU.
HOW-TO
- Install Maestro on your local computer. Detailed instructions can be found on our Maestro page.
- Draw / import the molecule you want to find similar molecules of
- Run the Maestro LigPrep tool on it
- Export the prepared molecule in the native Maestro format (mae), e.g. as
target.mae
- Copy the file to Puhti in your scratch area (Tips for copying files)
- Copy (and edit if necessary) the following script as
gpushape.bash
(don't copy the 139GB shape-file) to the same folder- This script will request 60 minutes of time on one GPU, use the shape file from
/appl/data/bio/molport-shape/MP_SHAPE.bin
, usetarget.mae
as the search molecule, and put the results inshape_test-out.maegz
- This script will request 60 minutes of time on one GPU, use the shape file from
- Initialize the default Maestro installation with
- ...and submit the job (note, without
sbatch
!) - Copy the results to your local computer for analysis