Maxwell : alphapulldown

AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multime

Using alphapulldown on Maxwell

Use the alphapulldown module to setup the environment. The module will also set the environment for alphafold 2.2.2, cuda 11.3 and the databases required to run alphafold. The setup is somewhat experimental also ignoring the python==3.7 requirement of alphapulldown, but seems to work fine otherwise. Sample batch-scripts for example_1 of alphapulldown can be found in  /software/alphapulldown/examples/.

module load maxwell alphapulldown

• alphapulldown <0.30.7 uses /beegfs/desy/group/it/ReferenceData/alphafold as DATADIR and the alphafold installation in /software/alphafold/2.2.2L
• alphapulldown >=0.30.7 uses /beegfs/desy/group/it/ReferenceData/alphafold2.3 as DATADIR and comes with its own alphafold installation
  • v0.30.7: alphafold 2.3.2
• Note: alphapulldown uses python==3.8

Examples

sample batch-scripts can be found in /software/alphapulldown/examples/sbatch-predict.sh