From bcfd36c046c2d5b1ac2ed7b07bca4f8df3f5d9f5 Mon Sep 17 00:00:00 2001 From: Jun Liu Date: Thu, 28 May 2026 11:25:08 +0800 Subject: [PATCH] Update README.md --- README.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index d645a8f..1881fe2 100644 --- a/README.md +++ b/README.md @@ -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 ```