Create README.md

README.md

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+
+# PPLM
+
+![PPLM Banner]([https://via.placeholder.com/1200x200?text=PPLM](https://zhanglab.comp.nus.edu.sg/PPLM/img/pipeline.png)) <!-- 可以换成真实Banner -->
+
+---
+
+**Version 1.0, 03/25/2025**  
+(Copyrighted by the Regents of the National University of Singapore, All rights reserved)
+
+PPLM is a protein–protein language model that learns directly from paired sequences through a novel
+attention architecture, explicitly capturing inter-protein context. Building on PPLM, we developed
+PPLM-PPI, PPLM-Affinity, and PPLM-Contact for predicting protein–protein interactions, estimating
+binding affinity, and identifying interface residue contacts, respectively.
+
+**Authors**: Jun Liu, Hungyu Chen, and Yang Zhang
+
+**Contact**: junl_sg@nus.edu.sg
+
+**Citation**:  
+> Jun Liu, Hungyu Chen, Yang Zhang. A Protein-Protein Language Model for Interaction, Binding Affinity, and Interface Contact Prediction. *In preparation.*
+
+**Webserver**: [PPLM Online Submission](https://zhanglab.comp.nus.edu.sg/PPLM/)  
+
+**License**: PolyForm Noncommercial License
+
+---
+
+## System Requirements
+- x86_64 machine
+- Linux Kernel OS
+
+## Software & Dataset Requirements (for PPLM-Contact)
+1. **HH-suite3** for MSA Search: [Install HH-suite3](https://github.com/soedinglab/hh-suite)
+2. **Uniclust Database**: [Download Uniclust](http://wwwuser.gwdg.de/~compbiol/uniclust/2021_03/)
+3. **CCMpred** for DCA: [Install CCMpred](https://github.com/soedinglab/CCMpred)
+4. **LoadHHM** for PSSM Calculation: [LoadHHM.py](https://github.com/j3xugit/RaptorX-Contact/blob/master/Common/LoadHHM.py)
+5. **ESM-MSA** for Feature Generation: [Install ESM](https://github.com/facebookresearch/esm)
+
+## Usage
+```bash
+# 1. Install environment
+conda env create -f environment.yml
+
+# 2. Activate environment
+conda activate PPLM
+
+# 3. Run PPLM-PPI
+python run_pplm-ppi.py example/seq_pairs.fasta example/seq_pairs.results
+
+# 4. Run PPLM-Affinity
+python run_pplm-affinity.py example/receptor.fasta example/ligand.fasta
+
+# 5. Run PPLM-Contact (homodimer)
+python run_pplm-contact.py example/protein.pdb example/protein.pdb example/homo_example
+
+# 6. Run PPLM-Contact (heterodimer)
+python run_pplm-contact.py example/protein1.pdb example/protein2.pdb example/hetero_example
+
+# 7. Generate embeddings and attention weights
+python run_pplm.py example/seq1.fasta example/seq2.fasta example/seq1-seq2.pplm.pkl
+```
+
+## Example Outputs
+
+### PPLM-PPI
+- Command:
+```bash
+python run_pplm-ppi.py example/seq_pairs.fasta example/seq_pairs.results
+```
+- Output format (example):
+```
+>Protein1:Protein2
+Interaction Probability
+```
+
+### PPLM-Affinity
+- Command:
+```bash
+python run_pplm-affinity.py example/receptor.fasta example/ligand.fasta
+```
+- Output: Predicted binding affinity printed to the command line.
+
+### PPLM-Contact
+- Command:
+```bash
+python run_pplm-contact.py example/protein.pdb example/protein.pdb example/homo_example
+```
+- Output file: `homo_example/homo_example.pred_contact.txt`
+
+Format:
+| Rank | ResIdx1 | ResType1 | ResIdx2 | ResType2 | Contact Probability |
+|:----:|:-------:|:--------:|:-------:|:--------:|:-------------------:|
+
+---
+
+*This README was automatically generated.*