This examples is based of the rDock tutorial that is adapted to use data from CDK2 (cyclin dependent kinase 2). It uses data from the DUD_rDock_TestSet.
Nextflow and Docker (or Singularity) must be installed on the host machine.
Copy the relevant files from /datasets/DUD_rDock_TestSet.
./1_copy_files.shrDock needs a cavity defintion. In this case we use the rbcavity program that uses a cound ligand to define the cavity.
./2_create_cavity.shThe results are the cdk2_rdock_cav1.grd and cdk2_rdock.as files.
This runs the rbcavity in the informaticsmatters/rdock/ Docker image.
This runs the docking using Nextflow which executes each of the stages, parallelising the computationally demanding process of doing the actual dockings according to the number of cores on the machine. See the rdock.nf file for details.
./3_run_rdock.shThe result is the rdock_results.sdf.gz file.
This uses the informaticsmatters/rdkit_pipelines/ and informaticsmatters/rdock-mini/ Docker images.
Note this will take some time depending on the power of your computer. To perform 100 dockings on the entire dataset takes about 10 hours on a 24 core machine. To run smaller jobs see the comments in the 2_run_rdock.sh file.
Note this workflow can also be run using Singularity. Look at the 2_create_cavity.sh and 3_run_rdock.sh
scripts and change -with-docker to -with-singularity