[
{
"id": "example_1/5L33",
"label": "1 · Monomer / 5L33",
"description": "Official submit_example_1.sh, applied to 5L33. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_1.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/5L33.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_1/6MRR",
"label": "1 · Monomer / 6MRR",
"description": "Official submit_example_1.sh, applied to 6MRR. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_1.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/6MRR.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_2/3HTN",
"label": "2 · Design chains A and B / 3HTN",
"description": "Official submit_example_2.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_2.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_2/4YOW",
"label": "2 · Design chains A and B / 4YOW",
"description": "Official submit_example_2.sh, applied to 4YOW. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_2.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/4YOW.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_3/3HTN",
"label": "3 · Single PDB / 3HTN",
"description": "Official submit_example_3.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_3.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_3_score_only/3HTN",
"label": "3 · Score native sequence / 3HTN",
"description": "Official submit_example_3_score_only.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_3_score_only.sh",
"values": {
"task": "score_only",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 10,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_3_score_only_from_fasta/3HTN",
"label": "3 · Score FASTA sequences / 3HTN",
"description": "Official submit_example_3_score_only_from_fasta.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_3_score_only_from_fasta.sh",
"values": {
"task": "score_only",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 5,
"sampling_temp": "0.1",
"seed": 13,
"batch_size": 1,
"path_to_fasta": "bio-tools://proteinmpnn/outputs/example_3_outputs/seqs/3HTN.fa"
}
},
{
"id": "example_4/3HTN",
"label": "4 · Fix selected positions / 3HTN",
"description": "Official submit_example_4.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_4.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
"A": [
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],
"C": [
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14,
15,
16,
17,
18,
19,
20,
40
]
}
}
},
{
"id": "example_4_non_fixed/3HTN",
"label": "4 · Design selected positions / 3HTN",
"description": "Official submit_example_4_non_fixed.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_4_non_fixed.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
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142,
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]
}
}
},
{
"id": "example_5/3HTN",
"label": "5 · Tie selected positions / 3HTN",
"description": "Official submit_example_5.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_5.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
"A": [
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],
"C": [
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]
},
"tied_positions_jsonl": [
{
"A": [
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"C": [
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]
},
{
"A": [
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],
"C": [
2
]
},
{
"A": [
3
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"C": [
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]
},
{
"A": [
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],
"C": [
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]
},
{
"A": [
5
],
"C": [
5
]
},
{
"A": [
6
],
"C": [
6
]
},
{
"A": [
7
],
"C": [
7
]
},
{
"A": [
8
],
"C": [
8
]
}
]
}
},
{
"id": "example_4/4YOW",
"label": "4 · Fix selected positions / 4YOW",
"description": "Official submit_example_4.sh, applied to 4YOW. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_4.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/4YOW.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
"A": [
1,
2,
3,
4,
5,
6,
7,
8,
23,
25
],
"C": [
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
40
]
}
}
},
{
"id": "example_4_non_fixed/4YOW",
"label": "4 · Design selected positions / 4YOW",
"description": "Official submit_example_4_non_fixed.sh, applied to 4YOW. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_4_non_fixed.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/4YOW.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
"A": [
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15,
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28,
29,
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33,
34,
35,
36,
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213,
214,
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216,
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221,
222,
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225,
226,
227
],
"C": [
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202,
203,
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205,
206,
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208,
209,
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212,
213,
214,
215,
216,
217,
218,
219,
220,
221,
222,
223,
224,
225,
226,
227
]
}
}
},
{
"id": "example_5/4YOW",
"label": "5 · Tie selected positions / 4YOW",
"description": "Official submit_example_5.sh, applied to 4YOW. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_5.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/4YOW.pdb",
"pdb_path_chains": "A C",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"fixed_positions_jsonl": {
"A": [
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
23
],
"C": [
10,
11,
18,
19,
20,
22
]
},
"tied_positions_jsonl": [
{
"A": [
1
],
"C": [
1
]
},
{
"A": [
2
],
"C": [
2
]
},
{
"A": [
3
],
"C": [
3
]
},
{
"A": [
4
],
"C": [
4
]
},
{
"A": [
5
],
"C": [
5
]
},
{
"A": [
6
],
"C": [
6
]
},
{
"A": [
7
],
"C": [
7
]
},
{
"A": [
8
],
"C": [
8
]
}
]
}
},
{
"id": "example_6/4GYT",
"label": "6 · Homo-oligomer / 4GYT",
"description": "Official submit_example_6.sh, applied to 4GYT. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_6.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_homooligomers/pdbs/4GYT.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.2",
"seed": 37,
"batch_size": 1,
"homo_oligomer": true
}
},
{
"id": "example_6/6EHB",
"label": "6 · Homo-oligomer / 6EHB",
"description": "Official submit_example_6.sh, applied to 6EHB. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_6.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_homooligomers/pdbs/6EHB.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.2",
"seed": 37,
"batch_size": 1,
"homo_oligomer": true
}
},
{
"id": "example_7/5L33",
"label": "7 · Unconditional probabilities / 5L33",
"description": "Official submit_example_7.sh, applied to 5L33. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_7.sh",
"values": {
"task": "unconditional_probs_only",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/5L33.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 1,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_8/5L33",
"label": "8 · Polar amino-acid bias / 5L33",
"description": "Official submit_example_8.sh, applied to 5L33. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_8.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/5L33.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"bias_AA_jsonl": {
"D": 1.39,
"E": 1.39,
"H": 1.39,
"K": 1.39,
"N": 1.39,
"Q": 1.39,
"R": 1.39,
"S": 1.39,
"T": 1.39,
"W": 1.39,
"Y": 1.39
}
}
},
{
"id": "example_7/6MRR",
"label": "7 · Unconditional probabilities / 6MRR",
"description": "Official submit_example_7.sh, applied to 6MRR. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_7.sh",
"values": {
"task": "unconditional_probs_only",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/6MRR.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 1,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1
}
},
{
"id": "example_8/6MRR",
"label": "8 · Polar amino-acid bias / 6MRR",
"description": "Official submit_example_8.sh, applied to 6MRR. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_8.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_monomers/pdbs/6MRR.pdb",
"pdb_path_chains": "",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"bias_AA_jsonl": {
"D": 1.39,
"E": 1.39,
"H": 1.39,
"K": 1.39,
"N": 1.39,
"Q": 1.39,
"R": 1.39,
"S": 1.39,
"T": 1.39,
"W": 1.39,
"Y": 1.39
}
}
},
{
"id": "example_pssm/3HTN",
"label": "PSSM · Guided design / 3HTN",
"description": "Official submit_example_pssm.sh, applied to 3HTN. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_pssm.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/3HTN.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"pssm_multi": 0.3,
"pssm_bias_flag": true,
"pssm_jsonl": "bio-tools://proteinmpnn/inputs/PSSM_inputs/3HTN.json"
}
},
{
"id": "example_pssm/4YOW",
"label": "PSSM · Guided design / 4YOW",
"description": "Official submit_example_pssm.sh, applied to 4YOW. Input files and the script’s sampling settings are included; folder examples run one structure per preset.",
"source_url": "https://github.com/dauparas/ProteinMPNN/blob/8907e6671bfbfc92303b5f79c4b5e6ce47cdef57/examples/submit_example_pssm.sh",
"values": {
"task": "design",
"pdb_path": "bio-tools://proteinmpnn/inputs/PDB_complexes/pdbs/4YOW.pdb",
"pdb_path_chains": "A B",
"num_seq_per_target": 2,
"sampling_temp": "0.1",
"seed": 37,
"batch_size": 1,
"pssm_multi": 0.3,
"pssm_bias_flag": true,
"pssm_jsonl": "bio-tools://proteinmpnn/inputs/PSSM_inputs/4YOW.json"
}
}
]