Nextflow pipelines for de novo protein binder design.
⚠️ NOTE: Major change inv0.2.0- individual workflows have been shifted intoworkflows/, all launched via a singlemain.nfentry point with the--methodflag. To modify any existing wrapper scripts, you should be able to simply usenextflow run Australian-Protein-Design-Initiative/nf-binder-design --method <method>. and keep other arguments the same.⚠️
- RFdiffusion → ProteinMPNN → AlphaFold2 initial guess → Boltz-2 refolding
- RFdiffusion Partial Diffusion → Boltz-2 refolding
- BindCraft (in parallel across multiple GPUs)
- BoltzGen (design proteins and peptides binders using BoltzGen)
- "Boltz Pulldown" (an AlphaPulldown-like protocol using Boltz-2)
⚠️ Note: Components of these workflows use RFdiffusion and BindCraft, which depend on PyRosetta/Rosetta, which is free for non-commercial use. Commercial use requires a paid license agreement with University of Washington: https://github.com/RosettaCommons/rosetta/blob/main/LICENSE.md and https://rosettacommons.org/software/licensing-faq/
Full documentation: https://australian-protein-design-initiative.github.io/nf-binder-design/
Install Nextflow.
Clone the git repository:
git clone https://github.com/Australian-Protein-Design-Initiative/nf-binder-designSee the examples directory for examples.
For any of the workflows, you can see the commandline options with --help, eg:
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method rfd --help
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method bindcraft --help
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method boltzgen --helpAvailable methods: rfd, rfd_partial, bindcraft, boltzgen, boltz_pulldown
Any of the --params commandline options can alternatively be defined in a params.json file and passed to the workflow with -params-file params.json.
Simple example (single 'local' compute node):
OUTDIR=results
mkdir -p $OUTDIR/logs
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method rfd \
--input_pdb target.pdb \
--outdir $OUTDIR \
--contigs "[A371-508/A753-883/A946-1118/A1135-1153/0 70-100]" \
--hotspot_res "A473,A995,A411,A421" \
--rfd_n_designs=10 \
--rfdiffusion_batch_size 1 \
-with-report $OUTDIR/logs/report_$(date +%Y%m%d_%H%M%S).html \
-with-trace $OUTDIR/logs/trace_$(date +%Y%m%d_%H%M%S).txt \
-resume \
-profile localIf you are working on a specific HPC cluster like M3 or MLeRP, you should omit
-profile localand add the-cflag pointing to the specific platform config, eg-c conf/platforms/m3.configfor M3.
See the rfd workflow documentation for more details on options available.
A more complex example, as a wrapper script for the M3 HPC cluster, using a the site-specific config (-c), a specific RFdiffusion model (--rfd_model_path), a radius of gyration filter on the generated RFdiffusion backbones (--rfd_filters), custom ProteinMPNN weights (--pmpnn_weigths) and radius of gyration potentials (--rfd_extra_args):
#!/bin/bash
# CHANGE THIS - this is the path where your git clone of this repo is
WF_PATH="/some/path/to/nf-binder-design"
mkdir -p results/logs
DATESTAMP=$(date +%Y%m%d_%H%M%S)
# Ensure our tmp directory is in a location with enough space
export TMPDIR=$(realpath ./tmp)
export NXF_TEMP=$TMPDIR
mkdir -p $TMPDIR
# CHANGE THIS to a path in scratch or scratch2 to act as the cache directory for apptainer
# Containers will be automatically downloaded to this path.
# You can add it to ~/.bashrc if you prefer
export NXF_APPTAINER_CACHEDIR=/some/path/to/scratch2/apptainer_cache
export NXF_APPTAINER_TMPDIR=$TMPDIR
# There's a module for Nextflow on M3
module load nextflow/24.04.3 || true
# CHANGE the --slurm_account to match the project ID you wish to run SLURM jobs under
nextflow \
-c ${WF_PATH}/conf/platforms/m3.config run \
${WF_PATH}/main.nf \
--method rfd \
--slurm_account=ab12 \
--input_pdb 'input/target_cropped.pdb' \
--design_name my-binder \
--outdir results \
--contigs "[B346-521/B601-696/B786-856/0 70-130]" \
--hotspot_res "B472,B476,B484,B488" \
--rfd_n_designs=1000 \
--rfd_batch_size=5 \
--rfd_filters="rg<20" \
--pmpnn_seqs_per_struct=2 \
--pmpnn_relax_cycles=1 \
--pmpnn_weigths="/models/HyperMPNN/retrained_models/v48_020_epoch300_hyper.pt" \
--rfd_model_path="/models/rfdiffusion/Complex_beta_ckpt.pt" \
--rfd_extra_args='potentials.guiding_potentials=[\"type:binder_ROG,weight:7,min_dist:10\"] potentials.guide_decay="quadratic"' \
-resume \
-with-report results/logs/report_${DATESTAMP}.html \
-with-trace results/logs/trace_${DATESTAMP}.txtSee the M3 HPC cluster examples for more examples specific to running on SLURM.
NOTE: It seems with output from previous designs that the binder is always named chain A, and your other chains are named B, C, etc - irrespective of the chain ID in the original target PDB file. Residue numbering is 1 to N, sequential irrespective of gaps in the chain, rather than original target chain numbering.
OUTDIR=results
mkdir -p $OUTDIR/logs
# Generate 10 partial designs for each binder, in batches of 5
# Note the 'single quotes' around the '*.pdb' glob pattern !
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method rfd_partial \
--input_pdb 'my_designs/*.pdb' \
--rfd_n_partial_per_binder=10 \
--rfd_batch_size=5 \
--hotspot_res "A473,A995,A411,A421" \
--rfd_partial_T=2,5,10,20 \
-with-report $OUTDIR/logs/report_$(date +%Y%m%d_%H%M%S).html \
-with-trace $OUTDIR/logs/trace_$(date +%Y%m%d_%H%M%S).txt \
-profile localSee the rfd_partial workflow documentation for more details on options available.
The --method bindcraft workflow helps run BindCraft trajectories in parallel across multiple GPUs.
This is particularly well suited for running BindCraft on an HPC cluster, or a workstation with multiple GPUs.
Unlike the default BindCraft configuration which runs for an indeterminate amount of time until a number of accepted designs are found,
this pipeline will run a fixed number of trajectories --bindcraft_n_traj and stop.
Example:
DATESTAMP=$(date +%Y%m%d_%H%M%S)
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method bindcraft \
--input_pdb 'input/PDL1.pdb' \
--outdir results \
--target_chains "A" \
--hotspot_res "A56,A125" \
--hotspot_subsample 0.5 \
--binder_length_range "55-120" \
--bindcraft_n_traj 2 \
--bindcraft_batch_size 1 \
--bindcraft_advanced_settings_preset "default_4stage_multimer" \
--bindcraft_filters_preset "default_filters" \
-profile local \
-resume \
-with-report results/logs/report_${DATESTAMP}.html \
-with-trace results/logs/trace_${DATESTAMP}.txt--bindcraft_advanced_settings_preset and --bindcraft_filters_preset are are those available in the BindCraft settings_advanced and settings_filters directories (without the .json extension).
--hotspot_subsample randomly takes this random proportion of the hotspot residues for each design, allowing the impact of hotspot selection to be explored in a single run.
If you have multiple GPUs per compute node, you can specify them with the --gpu_devices flag, eg --gpu_devices=0,1.
Results are saved to the --outdir directory, in the bindcraft subdirectory, with CSV outputs from each batch combined into single tables, eg bindcraft/final_design_stats.csv.
A report summarizing the results is generated in bindcraft_report.html.
See the bindcraft workflow documentation for more details on options and output.
The --method boltzgen workflow automates the design of binders using the BoltzGen generative model.
It supports protein-anything, peptide-anything, protein_small-molecule and nanobody-anything protocols.
Example:
nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
--method boltzgen \
--config_yaml config/my_design.yaml \
--outdir results \
--num_designs 100 \
--batch_size 10 \
--devices 1See the boltzgen workflow documentation for more details on configuration files and options.
MIT
Note that some software dependencies of the pipeline are under less permissive licenses - in particular, RFdiffusion and BindCraft use Rosetta/PyRosetta which is only free for Non-Commercial use.