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Jun Liu
2025-07-04 16:59:24 +08:00
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@@ -75,14 +75,24 @@ python pplm_ppi/predict.py example/seq1.fasta example/seq2.fasta
```bash
python run_pplm-affinity.py example/receptor.fasta example/ligand.fasta
```
### 5. Run PPLM-Contact (homodimer)
### 5. Run PPLM-Contact
For homodimer
```bash
python run_pplm-contact.py example/protein.pdb example/protein.pdb example/homo_example
```
### 6. Run PPLM-Contact (heterodimer)
For heterodimer
```bash
python run_pplm-contact.py example/protein1.pdb example/protein2.pdb example/hetero_example
```
### 5. Run PPLM-Contact2
For homodimer
```bash
python run_pplm-contact2.py example/homodimer.afm.pdb example/homodimer.af3.pdb example/homodimer.dmf.pdb example/homo_example2
```
For heterodimer
```bash
python run_pplm-contact2.py example/heterodimer.afm.pdb example/heterodimer.af3.pdb example/heterodimer.dmf.pdb example/hetero_example2
```
### 7. Generate embeddings and attention weights for other applications
```bash
python run_pplm.py example/seq1.fasta example/seq2.fasta example/seq1-seq2.pplm.pkl