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Jun Liu
2025-10-31 14:12:31 +08:00
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@@ -38,6 +38,14 @@ binding affinity, and identifying interface residue contacts, respectively.
5. **ESM-MSA** for Feature Generation: Install the [ESM package](https://github.com/facebookresearch/esm), or use the pre-packaged version within "pplm_contact/external_tools" directory. Download the pre-trained [ESM-MSA model](https://dl.fbaipublicfiles.com/fair-esm/models/esm_msa1_t12_100M_UR50S.pt) and set the "esm_msa_model" parameter in the "config.py" file.
## Download parameters
You can download the pre-trained parameters of PPLM and its downstream models from the following link:
PPLM: [pplm_t33_650M.pt](https://1drv.ms/u/c/757b084e424e6c3f/EfSQ1FfvUFNInoQ52uCDFM8B74t3NKMZpSFeGjPLwJlqWA?e=XktDrg)
PPLM-PPI: [pplm-ppi_parameters.zip](https://1drv.ms/u/c/757b084e424e6c3f/EVyGul5qevZLpKhwgA7yLyUBOy-Wj8mGVmQKlGs0vviLhQ?e=MceTXU)
PPLM-Affinity: [pplm-affinity_parameters.zip](https://drive.google.com/file/d/19dB6-3UFoDW9Lz_Kmxk5gdHgAdvYTzyg/view?usp=drive_link)
PPLM-Contact: [pplm-contact_parameters.zip](https://onedrive.live.com/?id=%2Fpersonal%2F757b084e424e6c3f%2FDocuments%2FPPLM%2Fpplm%2Dcontact%5Fparameters%2Ezip&parent=%2Fpersonal%2F757b084e424e6c3f%2FDocuments%2FPPLM)
Please move the downloaded parameters to the models/ folder of pplm/, pplm_ppi/, pplm_affinity/, and pplm_contact/
/*
Run the download_parameter.sh script located in the models/ folder of pplm/, pplm_ppi/, pplm_affinity/, and pplm_contact/
```bash
cd pplm/models/ && bash download_model.sh
@@ -51,6 +59,7 @@ cd pplm_affinity/models/ && bash download_model.sh
```bash
cd pplm_contact/models/ && bash download_model.sh
```
*/
---
## Usage