[
{
"id": "unconditional_monomer",
"label": "Unconditional monomer",
"description": "Official example. One design per run.",
"source_url": "https://rosettacommons.github.io/foundry/models/rfd3/input.html",
"values": {
"input_mode": "parameters",
"job_name": "monomer",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": 150,
"is_non_loopy": true
}
},
{
"id": "demo",
"label": "demo (3 examples)",
"description": "Runs every named configuration in demo.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/demo.json",
"values": {
"job_name": "demo",
"inputs": "{\n \"M0255_1mg5_unfixed\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/M0255_1mg5.pdb\",\n \"ligand\": \"NAI,ACT\",\n \"unindex\": \"A108,A139,A152,A156\",\n \"length\": \"180-200\",\n \"select_fixed_atoms\": {\n \"A108\": \"ND2,CG\",\n \"A139\": \"OG,CB,CA\",\n \"A152\": \"OH,CZ\",\n \"A156\": \"NZ,CE,CD\",\n \"ACT\": \"OXT\",\n \"NAI\": \"\"\n },\n \"allow_ligand_on_existing_chain\": true\n },\n \"partial_diffusion\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/7v11.pdb\",\n \"ligand\": \"OQO\",\n \"partial_t\": 15.0,\n \"contig\": \"A431\",\n \"unindex\": \"A572-573\",\n \"select_fixed_atoms\": {\n \"A431\": \"TIP\",\n \"A572\": \"BKBN\",\n \"A573\": \"BKBN\"\n },\n \"allow_ligand_on_existing_chain\": true\n },\n \"dsDNA_basic\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/1bna.pdb\",\n \"contig\": \"A1-10,/0,B15-24,/0,120-130\",\n \"length\": \"140-150\",\n \"ori_token\": [\n 24,\n 20,\n 10\n ],\n \"is_non_loopy\": true\n }\n}",
"n_batches": 1,
"diffusion_batch_size": 1,
"input_mode": "text"
}
},
{
"id": "demo/M0255_1mg5_unfixed",
"label": "demo / M0255_1mg5_unfixed",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/demo.json",
"values": {
"input_mode": "parameters",
"job_name": "M0255_1mg5_unfixed",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "180-200",
"is_non_loopy": "",
"input": "bio-tools://rfd3/input_pdbs/M0255_1mg5.pdb",
"ligand": "NAI,ACT",
"unindex": "A108,A139,A152,A156",
"select_fixed_atoms": {
"A108": "ND2,CG",
"A139": "OG,CB,CA",
"A152": "OH,CZ",
"A156": "NZ,CE,CD",
"ACT": "OXT",
"NAI": ""
},
"allow_ligand_on_existing_chain": true
}
},
{
"id": "demo/partial_diffusion",
"label": "demo / partial_diffusion",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/demo.json",
"values": {
"input_mode": "parameters",
"job_name": "partial_diffusion",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "",
"is_non_loopy": "",
"input": "bio-tools://rfd3/input_pdbs/7v11.pdb",
"ligand": "OQO",
"partial_t": 15.0,
"contig": "A431",
"unindex": "A572-573",
"select_fixed_atoms": {
"A431": "TIP",
"A572": "BKBN",
"A573": "BKBN"
},
"allow_ligand_on_existing_chain": true
}
},
{
"id": "demo/dsDNA_basic",
"label": "demo / dsDNA_basic",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/demo.json",
"values": {
"input_mode": "parameters",
"job_name": "dsDNA_basic",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "140-150",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/1bna.pdb",
"contig": "A1-10,/0,B15-24,/0,120-130",
"ori_token": [
24,
20,
10
]
}
},
{
"id": "enzyme_design",
"label": "enzyme_design (1 example)",
"description": "Runs every named configuration in enzyme_design.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/enzyme_design.json",
"values": {
"job_name": "enzyme_design",
"inputs": "{\n \"M0255_1mg5_unfixed\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/M0255_1mg5.pdb\",\n \"ligand\": \"NAI,ACT\",\n \"unindex\": \"A108,A139,A152,A156\",\n \"length\": \"180-200\",\n \"select_fixed_atoms\": {\n \"A108\": \"ND2,CG\",\n \"A139\": \"OG,CB,CA\",\n \"A152\": \"OH,CZ\",\n \"A156\": \"NZ,CE,CD\",\n \"ACT\": \"OXT\",\n \"NAI\": \"\"\n },\n \"allow_ligand_on_existing_chain\": true\n }\n}",
"n_batches": 1,
"diffusion_batch_size": 1,
"input_mode": "text"
}
},
{
"id": "enzyme_design/M0255_1mg5_unfixed",
"label": "enzyme_design / M0255_1mg5_unfixed",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/enzyme_design.json",
"values": {
"input_mode": "parameters",
"job_name": "M0255_1mg5_unfixed",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "180-200",
"is_non_loopy": "",
"input": "bio-tools://rfd3/input_pdbs/M0255_1mg5.pdb",
"ligand": "NAI,ACT",
"unindex": "A108,A139,A152,A156",
"select_fixed_atoms": {
"A108": "ND2,CG",
"A139": "OG,CB,CA",
"A152": "OH,CZ",
"A156": "NZ,CE,CD",
"ACT": "OXT",
"NAI": ""
},
"allow_ligand_on_existing_chain": true
}
},
{
"id": "na_binder_design",
"label": "na_binder_design (5 examples)",
"description": "Runs every named configuration in na_binder_design.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"job_name": "na_binder_design",
"inputs": "{\n \"dsDNA_basic\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/1bna.pdb\",\n \"contig\": \"A1-10,/0,B15-24,/0,120-130\",\n \"length\": \"140-150\",\n \"ori_token\": [\n 24,\n 20,\n 10\n ],\n \"is_non_loopy\": true\n },\n \"ssDNA_basic\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/5o4d.pdb\",\n \"contig\": \"A1-23,/0,120-130\",\n \"length\": \"143-153\",\n \"ori_token\": [\n -5,\n -10,\n 8\n ],\n \"is_non_loopy\": true\n },\n \"ssDNA_diffused_from_dsDNA_pdb\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/1bna.pdb\",\n \"contig\": \"A1-10,/0,120-130\",\n \"length\": \"130-140\",\n \"select_fixed_atoms\": {\n \"A1-10\": \"\"\n },\n \"is_non_loopy\": true\n },\n \"RNA_basic\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/1q75.pdb\",\n \"contig\": \"A1-15,/0,120-130\",\n \"length\": \"135-145\",\n \"ori_token\": [\n 15,\n 2,\n -4\n ],\n \"is_non_loopy\": true\n },\n \"dsDNA_complex\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/2r5z.pdb\",\n \"contig\": \"C5-18,/0,D24-37,/0,40-50,A146-154,80-90\",\n \"length\": \"157-177\",\n \"unindex\": \"/0,/0,B251-255\",\n \"select_fixed_atoms\": {\n \"C9-14\": \"ALL\",\n \"D28-33\": \"ALL\",\n \"C5-8,C15-18\": \"\",\n \"D24-27,D34-37\": \"\"\n },\n \"ori_token\": [\n 25,\n 35,\n 20\n ],\n \"select_hbond_acceptor\": {\n \"C16\": \"N7,O6\",\n \"D31-32\": \"N7\",\n \"D28-30\": \"OP1,OP2,O3',O5'\"\n },\n \"select_hbond_donor\": {\n \"D31-32\": \"N6\"\n },\n \"is_non_loopy\": true\n }\n}",
"n_batches": 1,
"diffusion_batch_size": 1,
"input_mode": "text"
}
},
{
"id": "na_binder_design/dsDNA_basic",
"label": "na_binder_design / dsDNA_basic",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "dsDNA_basic",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "140-150",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/1bna.pdb",
"contig": "A1-10,/0,B15-24,/0,120-130",
"ori_token": [
24,
20,
10
]
}
},
{
"id": "na_binder_design/ssDNA_basic",
"label": "na_binder_design / ssDNA_basic",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "ssDNA_basic",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "143-153",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/5o4d.pdb",
"contig": "A1-23,/0,120-130",
"ori_token": [
-5,
-10,
8
]
}
},
{
"id": "na_binder_design/ssDNA_diffused_from_dsDNA_pdb",
"label": "na_binder_design / ssDNA_diffused_from_dsDNA_pdb",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "ssDNA_diffused_from_dsDNA_pdb",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "130-140",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/1bna.pdb",
"contig": "A1-10,/0,120-130",
"select_fixed_atoms": {
"A1-10": ""
}
}
},
{
"id": "na_binder_design/RNA_basic",
"label": "na_binder_design / RNA_basic",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "RNA_basic",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "135-145",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/1q75.pdb",
"contig": "A1-15,/0,120-130",
"ori_token": [
15,
2,
-4
]
}
},
{
"id": "na_binder_design/dsDNA_complex",
"label": "na_binder_design / dsDNA_complex",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/na_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "dsDNA_complex",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "157-177",
"is_non_loopy": true,
"input": "bio-tools://rfd3/input_pdbs/2r5z.pdb",
"contig": "C5-18,/0,D24-37,/0,40-50,A146-154,80-90",
"unindex": "/0,/0,B251-255",
"select_fixed_atoms": {
"C9-14": "ALL",
"D28-33": "ALL",
"C5-8,C15-18": "",
"D24-27,D34-37": ""
},
"ori_token": [
25,
35,
20
],
"select_hbond_acceptor": {
"C16": "N7,O6",
"D31-32": "N7",
"D28-30": "OP1,OP2,O3',O5'"
},
"select_hbond_donor": {
"D31-32": "N6"
}
}
},
{
"id": "protein_binder_design",
"label": "protein_binder_design (2 examples)",
"description": "Runs every named configuration in protein_binder_design.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/protein_binder_design.json",
"values": {
"job_name": "protein_binder_design",
"inputs": "{\n \"insulinr\": {\n \"dialect\": 2,\n \"infer_ori_strategy\": \"hotspots\",\n \"input\": \"bio-tools://rfd3/input_pdbs/4zxb_cropped.pdb\",\n \"contig\": \"40-120,/0,E6-155\",\n \"select_hotspots\": {\n \"E64\": \"CD2,CZ\",\n \"E88\": \"CG,CZ\",\n \"E96\": \"CD1,CZ\"\n },\n \"is_non_loopy\": true\n },\n \"pdl1\": {\n \"dialect\": 2,\n \"infer_ori_strategy\": \"hotspots\",\n \"input\": \"bio-tools://rfd3/input_pdbs/5o45_cropped.pdb\",\n \"contig\": \"50-120,/0,A17-131\",\n \"select_hotspots\": {\n \"A56\": \"CG,OH\",\n \"A115\": \"CG,SD\",\n \"A123\": \"CD2,OH\"\n },\n \"is_non_loopy\": true\n }\n}",
"n_batches": 1,
"diffusion_batch_size": 1,
"inference_sampler.step_scale": 3,
"inference_sampler.gamma_0": 0.2,
"input_mode": "text"
}
},
{
"id": "protein_binder_design/insulinr",
"label": "protein_binder_design / insulinr",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/protein_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "insulinr",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "",
"is_non_loopy": true,
"dialect": 2,
"infer_ori_strategy": "hotspots",
"input": "bio-tools://rfd3/input_pdbs/4zxb_cropped.pdb",
"contig": "40-120,/0,E6-155",
"select_hotspots": {
"E64": "CD2,CZ",
"E88": "CG,CZ",
"E96": "CD1,CZ"
},
"inference_sampler.step_scale": 3,
"inference_sampler.gamma_0": 0.2
}
},
{
"id": "protein_binder_design/pdl1",
"label": "protein_binder_design / pdl1",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/protein_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "pdl1",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "",
"is_non_loopy": true,
"dialect": 2,
"infer_ori_strategy": "hotspots",
"input": "bio-tools://rfd3/input_pdbs/5o45_cropped.pdb",
"contig": "50-120,/0,A17-131",
"select_hotspots": {
"A56": "CG,OH",
"A115": "CG,SD",
"A123": "CD2,OH"
},
"inference_sampler.step_scale": 3,
"inference_sampler.gamma_0": 0.2
}
},
{
"id": "sm_binder_design",
"label": "sm_binder_design (2 examples)",
"description": "Runs every named configuration in sm_binder_design.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/sm_binder_design.json",
"values": {
"job_name": "sm_binder_design",
"inputs": "{\n \"buried\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/IAI.pdb\",\n \"length\": \"180-180\",\n \"ligand\": \"IAI\",\n \"select_fixed_atoms\": {\n \"IAI\": \"\"\n },\n \"select_buried\": {\n \"IAI\": \"C22,C23,C25,C24,C21,C20,N13,C15,C16,N14,C19,C11,N12,C18,C17,N9,O8,C4,C1,N3,C10,N5,C7,C2,C6,N27,O26,C33,C29,C32,O31,C30,N28\"\n }\n },\n \"partial\": {\n \"input\": \"bio-tools://rfd3/input_pdbs/IAI.pdb\",\n \"ligand\": \"IAI\",\n \"length\": \"180-180\",\n \"select_fixed_atoms\": {\n \"IAI\": \"\"\n },\n \"select_exposed\": {\n \"IAI\": \"C22,C23,C25,C24,C21,C20,N13,C15,C16,N14,C19,C11,N12,C18,C17\"\n },\n \"select_buried\": {\n \"IAI\": \"N9,O8,C4,C1,N3,C10,N5,C7,C2,C6,N27,O26,C33,C29,C32,O31,C30,N28\"\n }\n }\n}",
"n_batches": 1,
"diffusion_batch_size": 1,
"input_mode": "text"
}
},
{
"id": "sm_binder_design/buried",
"label": "sm_binder_design / buried",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/sm_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "buried",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "180-180",
"is_non_loopy": "",
"input": "bio-tools://rfd3/input_pdbs/IAI.pdb",
"ligand": "IAI",
"select_fixed_atoms": {
"IAI": ""
},
"select_buried": {
"IAI": "C22,C23,C25,C24,C21,C20,N13,C15,C16,N14,C19,C11,N12,C18,C17,N9,O8,C4,C1,N3,C10,N5,C7,C2,C6,N27,O26,C33,C29,C32,O31,C30,N28"
}
}
},
{
"id": "sm_binder_design/partial",
"label": "sm_binder_design / partial",
"description": "Official example with its bundled input structure. One design per run.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/sm_binder_design.json",
"values": {
"input_mode": "parameters",
"job_name": "partial",
"diffusion_batch_size": 1,
"n_batches": 1,
"length": "180-180",
"is_non_loopy": "",
"input": "bio-tools://rfd3/input_pdbs/IAI.pdb",
"ligand": "IAI",
"select_fixed_atoms": {
"IAI": ""
},
"select_exposed": {
"IAI": "C22,C23,C25,C24,C21,C20,N13,C15,C16,N14,C19,C11,N12,C18,C17"
},
"select_buried": {
"IAI": "N9,O8,C4,C1,N3,C10,N5,C7,C2,C6,N27,O26,C33,C29,C32,O31,C30,N28"
}
}
},
{
"id": "symmetry",
"label": "symmetry (6 examples)",
"description": "Runs every named configuration in symmetry.json, with one design per configuration.",
"source_url": "https://github.com/RosettaCommons/foundry/blob/b02eed6a6bdf8f44d14a80cc36e3da13c9f2291c/models/rfd3/docs/examples/symmetry.json",
"values": {
"job_name": "symmetry",
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}
]