ProteinMPNN

Inputs

• Place structure inputs (PDB plus ligand files) under /inputs.
• Batch mode: -I=<dir> (e.g. -I=/inputs) processes all input files in a folder.
• SubSeq supplies the matching model assets for the selected --model_type.
• Results are written to /outputs. Designed sequence FASTA files are written under /outputs/seqs.

Arguments

• --model_type: protein_mpnn, ligand_mpnn, per_residue_label_membrane_mpnn, global_label_membrane_mpnn, soluble_mpnn.
• --fasta_seq_separation: separator between chains in FASTA output.
• --verbose: print verbose logs.
• --pdb_path: input PDB path.
• --pdb_path_multi: JSON file listing PDB paths (keys used).
• --fixed_residues: residues to keep fixed (e.g. A12 A13 B2).
• --fixed_residues_multi: JSON mapping of fixed residues per PDB.
• --redesigned_residues: residues to redesign (everything else fixed).
• --redesigned_residues_multi: JSON mapping of redesigned residues per PDB.
• --bias_AA: global amino-acid bias string (e.g. A:-1.0,P:2.0).
• --bias_AA_per_residue: JSON mapping per-residue amino-acid biases.
• --bias_AA_per_residue_multi: JSON mapping per-PDB per-residue biases.
• --omit_AA: amino acids to omit globally (e.g. ACG).
• --omit_AA_per_residue: JSON mapping per-residue omissions.
• --omit_AA_per_residue_multi: JSON mapping per-PDB per-residue omissions.
• --symmetry_residues: symmetry groups (e.g. A12,A13|C2,C3).
• --symmetry_weights: weights corresponding to --symmetry_residues.
• --homo_oligomer: set to 1 to auto-configure homo-oligomer symmetry.
• --out_folder: normalized to /outputs.
• --file_ending: suffix appended to output filenames.
• --zero_indexed: set to 1 to start output numbering at 0.
• --seed: RNG seed.
• --batch_size: sequences per pass.
• --number_of_batches: number of batches to sample.
• --temperature: sampling temperature.
• --save_stats: set to 1 to save output stats.
• --ligand_mpnn_use_atom_context: set to 1 to use atom context.
• --ligand_mpnn_cutoff_for_score: protein-context cutoff in angstroms.
• --ligand_mpnn_use_side_chain_context: set to 1 to use side-chain context.
• --chains_to_design: chains to redesign (comma-separated).
• --parse_these_chains_only: chains to parse (comma-separated).
• --transmembrane_buried: buried residues for per-residue membrane model.
• --transmembrane_interface: interface residues for per-residue membrane model.
• --global_transmembrane_label: global label for global membrane model.
• --parse_atoms_with_zero_occupancy: set to 1 to parse zero-occupancy atoms.
• --pack_side_chains: set to 1 to run side-chain packing.
• --number_of_packs_per_design: packs per design.
• --sc_num_denoising_steps: denoising steps for packing.
• --sc_num_samples: samples per packing run.
• --repack_everything: set to 1 to repack fixed residues too.
• --force_hetatm: set to 1 to force ligand atoms as HETATM.
• --packed_suffix: suffix for packed PDBs.
• --pack_with_ligand_context: set to 1 to include ligand context during packing.
• --subseq_split_fastas: set to 1 to replace upstream multi-FASTA sequence outputs with separate single-record FASTA files under /outputs/seqs.
• --subseq_split_include_reference: set to 1 to include the first input/reference record under /outputs/seqs when splitting FASTA outputs.
• --subseq_clean_fasta_headers: set to 0 to preserve upstream FASTA headers; default 1 writes parser-safe IDs and /outputs/proteinmpnn_fasta_metadata.tsv.

Example arguments

Defaults that mirror the New Task prefill:

--model_type=protein_mpnn
-I=/inputs
--out_folder=/outputs
--temperature=0.05
--subseq_split_fastas=1
--subseq_clean_fasta_headers=1

Tweak --temperature or choose another --model_type for different design behavior.

Submit

Launch via New Task -> ProteinMPNN.

Output notes

• By default, SubSeq rewrites upstream FASTA headers to stable IDs like <source>_design_0001 and writes original headers plus parsed common stats to /outputs/proteinmpnn_fasta_metadata.tsv.
• When split FASTA output is off, the upstream multi-FASTA sequence output is preserved under /outputs/seqs. The first record is the input sequence when available.
• Use --subseq_split_fastas=1 to replace upstream multi-FASTA sequence files with per-design FASTA files under /outputs/seqs, named like <source>_design_0001.fasta.
• The first input/reference record is omitted from split outputs unless --subseq_split_include_reference=1 is set, in which case it is written as <source>_reference.fasta.
• For pipeline handoff, matching .seq.json files are written under /outputs/seqs/subseq_seqs. Chain-broken FASTA records such as binder:target are represented as multiple protein entities in one related sequence system, with parsed ProteinMPNN header scores written under metrics when available.
• For backbone-only inputs, the “input sequence” is often all glycine (not useful for many downstream tools).