https://github.com/ornl/affinity_pred

Protein-ligand affinity prediction using NLP
https://github.com/ornl/affinity_pred

artificial-intelligence machine-learning nlp

Last synced: about 1 year ago
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Protein-ligand affinity prediction using NLP

• Host: GitHub
• URL: https://github.com/ornl/affinity_pred
• Owner: ORNL
• License: bsd-3-clause
• Created: 2021-05-24T22:47:01.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2022-10-12T20:58:13.000Z (over 3 years ago)
• Last Synced: 2025-03-24T20:23:16.792Z (about 1 year ago)
• Topics: artificial-intelligence, machine-learning, nlp
• Language: Jupyter Notebook
• Homepage:
• Size: 967 KB
• Stars: 6
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# affinity_pred: Affinity prediction for protein-ligand complexes 

This repository implements a transformer model for binding affinity prediction of small molecules in complex with proteins, as described in the paper

[Language models for the prediction of SARS-CoV-2 inhibitors](https://doi.org/10.1177/10943420221121804)

Local installation

```

pip install git+https://github.com/ORNL/affinity_pred

```

Evaluation on Google Colab

- [Regex tokenizer model](./eval_regex.ipynb)[![Regex tokenizer model](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ORNL/affinity_pred/blob/master/eval_regex.ipynb)

- [BERT tokenizer model](./eval_bert.ipynb) [![BERT tokenizer model](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ORNL/affinity_pred/blob/master/eval_bert.ipynb)

Validation on SARS-CoV-2 Mpro experimental data

![alt text](https://github.com/ORNL/affinity_pred/blob/master/data/postera_pr_2.50.png?raw=true)

The model weights are downloaded from [Huggingface Hub](https://huggingface.co/jglaser)