https://github.com/astrabert/proteins-w-esm
Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale
https://github.com/astrabert/proteins-w-esm
ai bioinformatics huggingface-spaces masked-language-models protein-sequences protein-structure structure-prediction
Last synced: 6 months ago
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Predict the whole sequence and 3D structure of masked protein sequences with ESM by @evolutionaryscale
- Host: GitHub
- URL: https://github.com/astrabert/proteins-w-esm
- Owner: AstraBert
- License: other
- Created: 2024-06-28T22:12:48.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-06-29T00:54:02.000Z (over 1 year ago)
- Last Synced: 2025-04-12T14:05:18.940Z (6 months ago)
- Topics: ai, bioinformatics, huggingface-spaces, masked-language-models, protein-sequences, protein-structure, structure-prediction
- Language: Python
- Homepage:
- Size: 23.4 KB
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# Proteins with ESM
Predict the whole sequence and 3D structure of masked protein sequences with [ESM](https://github.com/evolutionaryscale/esm) by [Evolutionary Scale](https://www.evolutionaryscale.ai/).
## How to use it
### Locally - Build from scratch
> _The predictions are computationally-intense, you should have at least 16GB RAM and 4 core CPU_
1. Clone this repository:
```bash
git clone https://github.com/AstraBert/proteins-w-esm.git
cd proteins-w-esm
```
2. Rename `.env.example` to `.env` and modify it with your Hugging Face access token (`read` or `write` permissions, `fine-grained` is nut supported)
3. Launch the application and wait for it to load on `http://localhost:7860`
```bash
python3 app.py
```
### Locally - Use Docker image
1. Pull Docker image
```bash
docker pull astrabert/proteinswithesm:latest
```
2. Run the image and wait for it to load on `http://localhost:7860`:
```bash
docker run -p 7860:7860 astrabert/proteinswithesm:latest
```
### Online - Hugging Face demo
Use directly the Hugging Face Space demo that you can find [here](https://huggingface.co/spaces/as-cle-bert/proteins-with-esm).
### Online - Use GitHub CodeSpaces
Click the `<> Code` green button and then click on `CodeSpaces -> Create CodeSpace on 'main'`.
You should be redirected to a VSCode-based space connected to the port on which the app runs, directly accessible under the "Ports" section of the VSCode interface.