nf-binder-design

name	nf-binder-design
description	Runs the nf-binder-design Nextflow pipeline for de novo protein binder design. Covers RFdiffusion (--method rfd), partial diffusion (--method rfd_partial), RFdiffusion3 (--method rfd3), BindCraft (--method bindcraft), Germinal (--method germinal), BoltzGen (--method boltzgen), Boltz Pulldown (--method boltz_pulldown), and FoldSeek (--method foldseek or --do_foldseek). Use when the user wants to design protein binders, nanobodies, or peptides, set up or run nf-binder-design, configure HPC/SLURM, or troubleshoot pipeline errors.
priority	5

nf-binder-design

You are an expert at running the nf-binder-design Nextflow pipeline for de novo protein binder design.

Your job is to help the user choose the right workflow, construct correct nextflow run commands, set up HPC execution, and interpret outputs.

GitHub: https://github.com/Australian-Protein-Design-Initiative/nf-binder-design Docs: https://australian-protein-design-initiative.github.io/nf-binder-design/ Examples: examples/pdl1-rfd/, examples/pdl1-rfd3/, examples/pdl1-bindcraft/, examples/pdl1-boltzgen/, examples/pdl1-germinal/

When to Use This Skill

Activate when the user mentions nf-binder-design, protein binder design, RFdiffusion, RFDiffusion3, ProteinMPNN, AF2 initial guess, Boltz-2, BindCraft, Germinal, BoltzGen, or FoldSeek.

Examples:

• "Design me a binder targeting PDL1"
• "Run nf-binder-design on HPC"
• "Create nanobodies with BoltzGen"
• "Design de novo binders with RFDiffusion3"
• "Troubleshoot RFdiffusion pipeline"

Quick Start

Create a separate working directory per run:

mkdir -p {project}/runs/{method}/{target}_hotspots_A56
cd {project}/runs/{method}/{target}_hotspots_A56

Invoke via a single entry point:

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method <method> [options]

From a local git clone: nextflow run /path/to/nf-binder-design/main.nf --method <method> [options]

Method-specific help: add --method <method> --help

First-time setup

If the user does not have a working Nextflow installation, follow the ordered checklist in references/setup-and-hpc.md:

1. java -version (need Java 17+)
2. nextflow info (install Nextflow if missing — Seqera install guide)
3. Check/pull pipeline (~/.nextflow/assets/... or nextflow pull)
4. Smoke test: --method rfd --help
5. Choose profile: -profile local (workstation GPU) vs -profile slurm / site profile (HPC)

→ Full install, profile, and HPC details: references/setup-and-hpc.md

Utility Scripts

Helper scripts live in the pipeline bin/ directory. Run with uv:

Git clone — from the repo root:

cd /path/to/nf-binder-design
uv run bin/get_contigs.py --help

After nextflow pull — scripts are in the Nextflow assets cache:

uv run ~/.nextflow/assets/Australian-Protein-Design-Initiative/nf-binder-design/bin/get_contigs.py --help

Use the bin/ from the same pipeline version you intend to run. See references/setup-and-hpc.md for the full utility script table.

Script	Use for
get_contigs.py	Extract contigs from a cropped PDB (rfd, rfd3)
trim_to_contigs.py	Trim a structure to contigs (bindcraft, boltzgen)
renumber_chains.py	Renumber residues from 1 (boltzgen)

→ Target preparation checklist: references/target-preparation.md

Available Methods

Method	Description	Key Use Case
rfd	RFdiffusion → ProteinMPNN → AF2 initial guess → Boltz-2 refolding	Standard de novo binder design
rfd_partial	Partial diffusion refinement	Optimise/diversify existing binder designs
rfd3	RFdiffusion3 → MPNN → RosettaFold3 → optional Boltz refold	De novo design with RFDiffusion3
bindcraft	BindCraft in parallel	End-to-end design with built-in validation
germinal	Germinal in parallel	Antibody and nanobody design via Hydra YAML
boltzgen	BoltzGen generative model	Protein, peptide, nanobody, or small-molecule binders
boltz_pulldown	Boltz-2 multimer predictions	Validate designed binders (AlphaPulldown-like)
foldseek	FoldSeek structural search	Annotate designs against CATH/PDB databases

Add --do_foldseek to rfd, rfd3, bindcraft, or boltzgen to run FoldSeek on outputs inline.

Choosing a Method

1. New binder from scratch? → rfd (established) or bindcraft (end-to-end) or boltzgen (protein/peptide/nanobody/small-molecule)
2. Antibody or nanobody? → germinal (Hydra YAML) or boltzgen with nanobody-anything
3. Refine existing designs? → rfd_partial
4. Validate binder sequences? → boltz_pulldown
5. Annotate structural similarity? → --do_foldseek or --method foldseek

Common Flags (All Methods)

--outdir results
-profile local          # Workstation with local GPU
-profile slurm          # SLURM HPC (generic)
-profile slurm,m3       # SLURM + site-specific (see setup-and-hpc.md)
-profile nci_gadi       # NCI Gadi (PBS Pro)
-resume
-with-report results/logs/report_$(date +%Y%m%d_%H%M%S).html
-with-trace results/logs/trace_$(date +%Y%m%d_%H%M%S).txt
-params-file params.json

Profiles: See references/setup-and-hpc.md for the full decision tree (local vs SLURM vs PBS vs HyperQueue vs custom -c config).

Method Examples

One minimal example per method. See the matching references/*-workflow.md for advanced options, filters, refolding, and HPC examples.

rfd (RFdiffusion)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method rfd \
  --input_pdb 'input/target.pdb' \
  --outdir results \
  --contigs "[A18-132/0 65-120]" \
  --hotspot_res "A56" \
  --rfd_n_designs 10 \
  -profile local -resume

→ references/rfd-workflow.md

rfd_partial (Partial Diffusion)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method rfd_partial \
  --input_pdb 'existing_designs/*.pdb' \
  --contigs "[A18-132/0 65-120]" \
  --hotspot_res "A56" \
  --rfd_n_partial_per_binder 10 \
  --rfd_partial_T "5,15" \
  -profile local -resume

Binder is chain A in rfd output; residue numbering is 1–N. → references/rfd-workflow.md

rfd3 (RFdiffusion3)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method rfd3 \
  --input_pdb input/target.pdb \
  --outdir results \
  --contigs "A17-131,/0,50-120" \
  --hotspot_res "A56,A115" \
  --rfd3_n_designs 10 \
  -profile local -resume

Config mode (atom-level hotspots): --rfd3_config input/rfd3_config.json. → references/rfd3-workflow.md

bindcraft (BindCraft)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method bindcraft \
  --input_pdb 'input/target.pdb' \
  --outdir results \
  --target_chains "A" \
  --hotspot_res "A56" \
  --binder_length_range "55-120" \
  --bindcraft_n_traj 100 \
  --bindcraft_batch_size 1 \
  -profile local -resume

→ references/bindcraft-workflow.md

germinal (Germinal)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method germinal \
  --germinal_config configs/target_vhh.yaml \
  --germinal_pdb_dir pdbs \
  --germinal_experiment_name target_vhh \
  --germinal_n_traj 4 \
  --germinal_batch_size 1 \
  --outdir results \
  -profile local -resume

→ references/germinal-workflow.md

boltzgen (BoltzGen)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method boltzgen \
  --config_yaml design.yaml \
  --outdir results \
  --protocol protein-anything \
  --num_designs 100 \
  --batch_size 10 \
  --budget 20 \
  -profile local -resume

Protocols: protein-anything, peptide-anything, protein-small_molecule, nanobody-anything. → references/boltzgen-workflow.md

boltz_pulldown (Boltz Pulldown)

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method boltz_pulldown \
  --input_fasta 'binders/*.fasta' \
  --target_fasta input/target.fasta \
  --outdir results \
  -profile local -resume

→ references/boltz-pulldown-workflow.md

foldseek (FoldSeek)

Standalone search on existing structures:

nextflow run Australian-Protein-Design-Initiative/nf-binder-design \
  --method foldseek \
  --input_pdbs 'results/designs/*.pdb' \
  --outdir results/foldseek \
  -profile local -resume

Or add --do_foldseek to a design workflow. → references/foldseek-workflow.md

Key Outputs

Method	Primary outputs
rfd / rfd_partial	combined_scores.tsv, binders.fasta, af2_initial_guess/pdbs/, boltz_refold/ (if enabled)
rfd3	rfd3/combined_scores.tsv, rfdiffusion3/output/, rosettafold3/output/
bindcraft	bindcraft/accepted/, bindcraft/bindcraft_report.html, bindcraft/final_design_stats.csv
germinal	germinal/accepted_designs.csv, germinal/accepted/structures/
boltzgen	boltzgen/filtered/final_ranked_designs/, boltzgen/merged/
boltz_pulldown	boltz_pulldown/boltz_pulldown.tsv, boltz_pulldown_report.html
foldseek	foldseek_results.tsv, foldseek_results_annotated.tsv (CATH databases)

Critical Gotchas

• Quote glob patterns — --input_pdb 'input/*.pdb' (not unquoted globs)
• Contig syntax — rfd: "[A18-132/0 65-120]" (v1); rfd3: "A17-131,/0,50-120" (v3, comma-separated)
• ~60 GB+ storage for containers; NVIDIA GPU required
• Rosetta licence — RFdiffusion and BindCraft use PyRosetta (non-commercial only)
• One pipeline per directory — exclusive lock on .nextflow/cache/; use separate run dirs
• Glycans near hotspots — check N-X-S/T sequons, PDB LINK records, UniProt PTM annotations
• VRAM — 12 GB → ~250 residues total; 24 GB → ~400; 32 GB → ~550 (target + max binder)
• BoltzGen YAML paths — use absolute paths in YAML configs (container working dir differs)

Setup and Troubleshooting

→ references/setup-and-hpc.md — installation, HPC/SLURM, environment variables → references/nextflow-troubleshooting.md — monitoring, failure diagnosis, common errors

Reference Files

Read on demand — do not load all upfront:

File	Contents
references/rfd-workflow.md	RFdiffusion, partial diffusion, filters, refolding, RMSD
references/rfd3-workflow.md	RFD3 params/config modes, MPNN, RF3, Boltz full-refold
references/bindcraft-workflow.md	BindCraft parameters, presets, VRAM
references/germinal-workflow.md	Germinal Hydra config, parallelisation
references/boltzgen-workflow.md	BoltzGen YAML, protocols, filtering
references/boltz-pulldown-workflow.md	Boltz Pulldown MSA options
references/foldseek-workflow.md	--do_foldseek flag and --method foldseek
references/target-preparation.md	Target viability and structure preparation
references/setup-and-hpc.md	Installation and HPC configuration
references/nextflow-troubleshooting.md	Monitoring and error diagnosis