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Merge pull request #93 from RosettaCommons/fix/ppi-docs

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docs: update the ppi docs
This commit is contained in:
Rohith Krishna
2025-12-10 20:54:56 -08:00
committed by GitHub
parent 50b9c4be46 092f2f5555
commit 27bf3f3e29
5 changed files with 37 additions and 15 deletions
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3
models/rfd3/docs/demo.json
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@@ -29,6 +29,7 @@
"input": "./input_pdbs/1bna.pdb",
"contig": "A1-10,/0,B15-24,/0,120-130",
"length": "140-150",
"ori_token": [24,20,10]
"ori_token": [24,20,10],
"is_non_loopy": true
}
}

15
models/rfd3/docs/na_binder_design.json
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@@ -3,25 +3,29 @@
"input": "./input_pdbs/1bna.pdb",
"contig": "A1-10,/0,B15-24,/0,120-130",
"length": "140-150",
"ori_token": [24,20,10]
"ori_token": [24,20,10],
"is_non_loopy": true
},
"ssDNA_basic": {
"input": "./input_pdbs/5o4d.pdb",
"contig": "A1-23,/0,120-130",
"length": "143-153",
"ori_token": [-5,-10,8]
"ori_token": [-5,-10,8],
"is_non_loopy": true
},
"ssDNA_diffused_from_dsDNA_pdb":{
"input": "./input_pdbs/1bna.pdb",
"contig": "A1-10,/0,120-130",
"length": "130-140",
"select_fixed_atoms": {"A1-10":""}
"select_fixed_atoms": {"A1-10":""},
"is_non_loopy": true
},
"RNA_basic": {
"input": "./input_pdbs/1q75.pdb",
"contig": "A1-15,/0,120-130",
"length": "135-145",
"ori_token": [15,2,-4]
"ori_token": [15,2,-4],
"is_non_loopy": true
},
"dsDNA_complex": {
"input": "./input_pdbs/2r5z.pdb",
@@ -36,7 +40,8 @@
},
"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"}
"select_hbond_donor": {"D31-32":"N6"},
"is_non_loopy": true
}
}

15
models/rfd3/docs/na_binder_design.md
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@@ -30,7 +30,8 @@ The length attribute should be the sum of all polymer lengths. in this case (120
"input": "./input_pdbs/1bna.pdb",
"contig": "A1-10,/0,B15-24,/0,120-130",
"length": "140-150",
"ori_token": [24,20,10]
"ori_token": [24,20,10],
"is_non_loopy": true
}
}
```
@@ -45,7 +46,8 @@ Similar to the previous example, but done for a PDB containing one DNA strand (A
"input": "./input_pdbs/5o4d.pdb",
"contig": "A1-23,/0,120-130",
"length": "143-153",
"ori_token": [-5,-10,8]
"ori_token": [-5,-10,8],
"is_non_loopy": true
}
}
```
@@ -59,7 +61,8 @@ Similar to the previous example but the input PDB has a dsDNA. One of the chains
"input": "./input_pdbs/1bna.pdb",
"contig": "A1-10,/0,120-130",
"length": "130-140",
"select_fixed_atoms": {"A1-10":""}
"select_fixed_atoms": {"A1-10":""},
"is_non_loopy": true
}
}
```
@@ -74,7 +77,8 @@ Example on RNA. Similar to the ssDNA example, example 2.
"input": "./input_pdbs/1q75.pdb",
"contig": "A1-15,/0,120-130",
"length": "135-145",
"ori_token": [15,2,-4]
"ori_token": [15,2,-4],
"is_non_loopy": true
}
}
```
@@ -104,7 +108,8 @@ To run this without warnings, you will need to install [hbplus](https://www.ebi.
},
"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"}
"select_hbond_donor": {"D31-32":"N6"},
"is_non_loopy": true
}
}

6
models/rfd3/docs/protein_binder_design.json
View File

@@ -8,7 +8,8 @@
"E64": "CD2,CZ",
"E88": "CG,CZ",
"E96": "CD1,CZ"
}
},
"is_non_loopy": true
},
"pdl1": {
"dialect": 2,
@@ -19,6 +20,7 @@
"A56": "CG,OH",
"A115": "CG,SD",
"A123": "CD2,OH"
}
},
"is_non_loopy": true
}
}

13
models/rfd3/docs/protein_binder_design.md
View File

@@ -5,6 +5,13 @@ RFD3 is a highly proficient protein binder designer. The following arguments hav
- infer_ori_strategy: how RFD3 decides to place the origin of the generated protein binder with respect to the target. We find that using the "hotspots" strategy works best
- select_hotspots: which atoms on the target should be bound (dictionary of residues on the target and atoms in those residues)
In addition, we strongly recommend the following setting, which encourages the model to make more structured designs:
- is_non_loopy: true
Some useful command-line overrides to experiment with include `inference_sampler.step_scale` (defaults to 1.5) and
`inference_sampler.gamma_0` (defaults to 0.6). Increasing the `step_scale` and decreasing `gamma_0` yields lower-temperature
designs, which tends to increase designability and decrease diversity.
If you would like to run the examples below, `protein_binder_design.json`, located in this directory, contains the example code. You can run it via:
```
rfd3 design out_dir=inference_outputs/protein_binder/0 \
@@ -35,7 +42,8 @@ The input files for the different examples are provided in `foundry/models/rfd3/
"E64": "CD2,CZ",
"E88": "CG,CZ",
"E96": "CD1,CZ",
}
},
"is_non_loopy": true
},
"pdl1": {
"dialect": 2,
@@ -46,7 +54,8 @@ The input files for the different examples are provided in `foundry/models/rfd3/
"A56": "CG,OH",
"A115": "CG,SD",
"A123": "CD2,OH",
}
},
"is_non_loopy": true
}
}
```