[
{
"id": "default",
"label": "Design examples 1: default",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "default",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "temperature",
"label": "Design examples 2: temperature",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "temperature",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"temperature": 0.05
}
},
{
"id": "random_seed",
"label": "Design examples 3: random seed",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "random-seed",
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "verbose",
"label": "Design examples 4: verbose",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "verbose",
"seed": 111,
"verbose": false,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "save_stats",
"label": "Design examples 5: save stats",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "save-stats",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"save_stats": true
}
},
{
"id": "fix_residues",
"label": "Design examples 6: fix residues",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "fix-residues",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"fixed_residues": "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10",
"bias_AA": "A:10.0"
}
},
{
"id": "redesign_residues",
"label": "Design examples 7: redesign residues",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "redesign-residues",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"redesigned_residues": "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10",
"bias_AA": "A:10.0"
}
},
{
"id": "batch_size",
"label": "Design examples 8: batch size",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "batch-size",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"batch_size": 3,
"number_of_batches": 5
}
},
{
"id": "global_bias",
"label": "Design examples 9: global bias",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "global-bias",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"bias_AA": "W:3.0,P:3.0,C:3.0,A:-3.0"
}
},
{
"id": "per_residue_bias",
"label": "Design examples 10: per residue bias",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "per-residue-bias",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"bias_AA_per_residue": {
"C1": {
"G": -0.3,
"C": -2.0,
"P": 10.8
},
"C3": {
"P": 10.0
},
"C5": {
"G": -1.3,
"P": 10.0
},
"C7": {
"G": -1.3,
"P": 10.0
}
}
}
},
{
"id": "global_omit",
"label": "Design examples 11: global omit",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "global-omit",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"omit_AA": "CDFGHILMNPQRSTVWY"
}
},
{
"id": "per_residue_omit",
"label": "Design examples 12: per residue omit",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "per-residue-omit",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"omit_AA_per_residue": {
"C1": "ACDEFGHIKLMNPQRSTVW",
"C3": "ACDEFGHIKLMNPQRSTVW",
"C5": "ACDEFGHIKLMNPQRSTVW",
"C7": "ACDEFGHIKLMNPQRSTVW"
}
}
},
{
"id": "symmetry",
"label": "Design examples 13: symmetry",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "symmetry",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"symmetry_residues": "C1,C2,C3|C4,C5|C6,C7",
"symmetry_weights": "0.33,0.33,0.33|0.5,0.5|0.5,0.5"
}
},
{
"id": "homooligomer",
"label": "Design examples 14: homooligomer",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "homooligomer",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/4GYT.pdb",
"homo_oligomer": true,
"number_of_batches": 2
}
},
{
"id": "file_ending",
"label": "Design examples 15: file ending",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "file-ending",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"file_ending": "_xyz"
}
},
{
"id": "zero_indexed",
"label": "Design examples 16: zero indexed",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "zero-indexed",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"zero_indexed": true,
"number_of_batches": 2
}
},
{
"id": "chains_to_design",
"label": "Design examples 17: chains to design",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "chains-to-design",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/4GYT.pdb",
"chains_to_design": "A,B"
}
},
{
"id": "parse_these_chains_only",
"label": "Design examples 18: parse these chains only",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "parse-these-chains-only",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/4GYT.pdb",
"parse_these_chains_only": "A,B"
}
},
{
"id": "ligandmpnn_default",
"label": "Design examples 19: ligandmpnn default",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "ligandmpnn-default",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "ligandmpnn_v_32_005_25",
"label": "Design examples 20: ligandmpnn v 32 005 25",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "ligandmpnn-v-32-005-25",
"checkpoint_ligand_mpnn": "ligandmpnn_v_32_005_25.pt",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "ligandmpnn_no_context",
"label": "Design examples 21: ligandmpnn no context",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "ligandmpnn-no-context",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"ligand_mpnn_use_atom_context": false
}
},
{
"id": "ligandmpnn_use_side_chain_atoms",
"label": "Design examples 22: ligandmpnn use side chain atoms",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "ligandmpnn-use-side-chain-atoms",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"ligand_mpnn_use_side_chain_context": true,
"fixed_residues": "C1 C2 C3 C4 C5 C6 C7 C8 C9 C10"
}
},
{
"id": "soluble_mpnn_default",
"label": "Design examples 23: soluble mpnn default",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "soluble_mpnn",
"job_name": "soluble-mpnn-default",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb"
}
},
{
"id": "global_label_membrane_mpnn_0",
"label": "Design examples 24: global label membrane mpnn 0",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "global_label_membrane_mpnn",
"job_name": "global-label-membrane-mpnn-0",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"global_transmembrane_label": "0"
}
},
{
"id": "per_residue_label_membrane_mpnn_default",
"label": "Design examples 25: per residue label membrane mpnn default",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "per_residue_label_membrane_mpnn",
"job_name": "per-residue-label-membrane-mpnn-default",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"transmembrane_buried": "C1 C2 C3 C11",
"transmembrane_interface": "C4 C5 C6 C22"
}
},
{
"id": "fasta_seq_separation",
"label": "Design examples 26: fasta seq separation",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "fasta-seq-separation",
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"fasta_seq_separation": ":"
}
},
{
"id": "pdb_path_multi",
"label": "Design examples 27: pdb path multi",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "pdb-path-multi",
"pdb_path_multi": {
"1BC8": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"4GYT": "bio-tools://ligandmpnn/inputs/4GYT.pdb"
},
"seed": 111
}
},
{
"id": "fixed_residues_multi",
"label": "Design examples 28: fixed residues multi",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "fixed-residues-multi",
"pdb_path_multi": {
"1BC8": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"4GYT": "bio-tools://ligandmpnn/inputs/4GYT.pdb"
},
"fixed_residues_multi": {
"1BC8": "C1 C2 C3 C4 C5 C10 C22",
"4GYT": "A7 A8 A9 A10 A11 A12 A13 B38"
},
"seed": 111
}
},
{
"id": "redesigned_residues_multi",
"label": "Design examples 29: redesigned residues multi",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "redesigned-residues-multi",
"pdb_path_multi": {
"1BC8": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"4GYT": "bio-tools://ligandmpnn/inputs/4GYT.pdb"
},
"redesigned_residues_multi": {
"1BC8": "C1 C2 C3 C4 C5 C10",
"4GYT": "A7 A8 A9 A10 A12 A13 B38"
},
"seed": 111
}
},
{
"id": "omit_AA_per_residue_multi",
"label": "Design examples 30: omit AA per residue multi",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "omit-AA-per-residue-multi",
"pdb_path_multi": {
"1BC8": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"4GYT": "bio-tools://ligandmpnn/inputs/4GYT.pdb"
},
"omit_AA_per_residue_multi": {
"1BC8": {
"C1": "ACDEFGHILMNPQRSTVWY",
"C2": "ACDEFGHILMNPQRSTVWY",
"C3": "ACDEFGHILMNPQRSTVWY"
},
"4GYT": {
"A7": "ACDEFGHILMNPQRSTVWY",
"A8": "ACDEFGHILMNPQRSTVWY"
}
},
"seed": 111
}
},
{
"id": "bias_AA_per_residue_multi",
"label": "Design examples 31: bias AA per residue multi",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "bias-AA-per-residue-multi",
"pdb_path_multi": {
"1BC8": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"4GYT": "bio-tools://ligandmpnn/inputs/4GYT.pdb"
},
"bias_AA_per_residue_multi": {
"1BC8": {
"C1": {
"A": 3.0,
"P": -2.0
},
"C2": {
"W": 10.0,
"G": -0.43
}
},
"4GYT": {
"A7": {
"Y": 5.0,
"S": -2.0
},
"A8": {
"M": 3.9,
"G": -0.43
}
}
},
"seed": 111
}
},
{
"id": "ligand_mpnn_cutoff_for_score",
"label": "Design examples 32: ligand mpnn cutoff for score",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "ligand-mpnn-cutoff-for-score",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"ligand_mpnn_cutoff_for_score": 6.0
}
},
{
"id": "insertion_code",
"label": "Design examples 33: insertion code",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "protein_mpnn",
"job_name": "insertion-code",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/2GFB.pdb",
"redesigned_residues": "B82 B82A B82B B82C",
"parse_these_chains_only": "B"
}
},
{
"id": "parse_atoms_with_zero_occupancy",
"label": "Design examples 34: parse atoms with zero occupancy",
"description": "Official README example; input files are bundled with the catalog.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#design-examples",
"values": {
"task": "design",
"model_type": "ligand_mpnn",
"job_name": "parse-atoms-with-zero-occupancy",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/inputs/1BC8.pdb",
"parse_atoms_with_zero_occupancy": true
}
},
{
"id": "autoregressive_score_w_seq",
"label": "Scoring examples 1: autoregressive score w seq",
"description": "Official scoring example using the bundled upstream output backbone, so a prior design run is not required.",
"source_url": "https://github.com/dauparas/LigandMPNN/blob/26ec57ac976ade5379920dbd43c7f97a91cf82de/README.md#scoring-examples",
"values": {
"task": "autoregressive_score",
"model_type": "ligand_mpnn",
"job_name": "autoregressive-score-w-seq",
"seed": 111,
"pdb_path": "bio-tools://ligandmpnn/outputs/ligandmpnn_default/backbones/1BC8_1.pdb",
"use_sequence": true,
"batch_size": 1,
"number_of_batches": 10
}
},
{
"id": "autoregressive_score_wo_seq",
"label": "Scoring examples 2: autoregressive score wo seq",
"description": "Official scoring example using the bundled upstream output backbone, so a prior design run is not required.",
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{
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{
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{
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}
]