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Jun Liu
2026-05-28 11:25:08 +08:00
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@@ -74,7 +74,11 @@ conda env create -f environment.yml
```bash
conda activate PPLM
```
### 3. Run PPLM-PPI
### 3. Download weights
```bash
cd weights && bash download_weights.sh
```
### 4.1. Run PPLM-PPI
```bash
python run_pplm-ppi.py example/seq1.fasta example/seq2.fasta
```
@@ -82,11 +86,11 @@ You can also run PPLM-PPI for two individual sequences:
```bash
python pplm_ppi/predict.py example/seq1.fasta example/seq2.fasta
```
### 4. Run PPLM-Affinity
### 4.1. Run PPLM-Affinity
```bash
python run_pplm-affinity.py example/receptor.fasta example/ligand.fasta
```
### 5. Run PPLM-Contact
### 4.3.1. Run PPLM-Contact
For homodimer
```bash
python run_pplm-contact.py example/protein.pdb example/protein.pdb example/homo_example
@@ -95,7 +99,7 @@ For heterodimer
```bash
python run_pplm-contact.py example/protein1.pdb example/protein2.pdb example/hetero_example
```
### 6. Run PPLM-Contact2
### 4.3.2. 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
@@ -104,7 +108,7 @@ 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 matrices for other applications
### 4.4. Generate embeddings and attention matrices for other applications
```bash
python run_pplm.py example/seq1.fasta example/seq2.fasta example/seq1-seq2.pplm.pkl
```