https://github.com/se7en69/proteinscape
ProteinScape is an interactive web-based tool that leverages the ESMFold API to predict and visualize the 3D structures of proteins from their amino acid sequences. Designed for researchers, educators, and students, ProteinScape provides an intuitive platform to explore protein structures and their associated features.
https://github.com/se7en69/proteinscape
bioinformatics prediction protein-structure streamlit-webapp webapplication
Last synced: 3 months ago
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ProteinScape is an interactive web-based tool that leverages the ESMFold API to predict and visualize the 3D structures of proteins from their amino acid sequences. Designed for researchers, educators, and students, ProteinScape provides an intuitive platform to explore protein structures and their associated features.
- Host: GitHub
- URL: https://github.com/se7en69/proteinscape
- Owner: se7en69
- License: mit
- Created: 2024-12-01T09:55:30.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-12-01T10:27:51.000Z (7 months ago)
- Last Synced: 2025-01-29T21:31:33.500Z (5 months ago)
- Topics: bioinformatics, prediction, protein-structure, streamlit-webapp, webapplication
- Language: Python
- Homepage: https://proteinscape.streamlit.app/
- Size: 89.8 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ProteinScape: Protein Structure Prediction Application
**ProteinScape** is a web-based application designed to predict and visualize the 3D structure of proteins from amino acid sequences. The app utilizes the **ESMFold API** to provide accurate structural predictions and includes an interactive interface for researchers, educators, and students to explore protein structures and their features.
## Features
- **Single Protein Structure Prediction**: Predict the 3D structure of a single protein sequence.
- **Multiple Protein Structure Prediction**: Predict the structure for multiple protein sequences (from FASTA file or manual input).
- **3D Visualization**: Interactive 3D visualization of predicted protein structures using `py3Dmol`.
- **Amino Acid Distribution Analysis**: Graphical display of the amino acid composition in the input sequence.
- **Sample Ramachandran Plot**: A sample Ramachandran plot showing the phi (ϕ) and psi (ψ) angles for each sequence.
## Tech Stack
- **Frontend**: Streamlit
- **Backend**: ESMFold API
- **Visualization**: py3Dmol
- **Plotting**: Matplotlib, Seaborn
- **Data Handling**: Pandas, Collections
- **Requests**: Python `requests` library for API calls
## Installation
1. **Clone the repository**:
```bash
git clone https://github.com/your-username/proteinscape.git
cd proteinscape
```
2. **Install the required dependencies**:
```bash
pip install -r requirements.txt
```
Ensure that the following Python packages are installed:
- `streamlit`
- `py3Dmol`
- `matplotlib`
- `seaborn`
- `pandas`
- `requests`
- `numpy`
3. **Run the application**:
```bash
streamlit run app.py
```
Open the provided `localhost` link in your browser.
## Usage
### Single Protein Structure Prediction
1. Enter a valid protein sequence (amino acids: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).
2. Click the "Predict Structure" button.
3. View the predicted 3D structure of the protein in the interactive viewer.
4. Download the predicted structure as a `.pdb` file.
5. View the amino acid distribution and a sample Ramachandran plot for further insights.
### Multiple Protein Structure Prediction
1. Upload a **FASTA** file with multiple protein sequences or manually input sequences in **FASTA** format.
2. The application will predict the structure for each sequence and allow visualization and downloading of each result.
3. Similar to single predictions, view the amino acid distribution and Ramachandran plot for each sequence.
### 3D Visualization
- Use the **py3Dmol** viewer to interact with the predicted protein structure.
- Select different visualization styles: `cartoon` or `stick`.
## API Information
The application uses the [ESMFold API](https://esmatlas.com/about) for protein structure prediction. The predicted output is displayed in `.pdb` format and is rendered in the web application for real-time interaction.
## Example
### Input
A valid protein sequence:
```
MKTAYIAKQRQISFVKSHFSRQDILDLWQYFSYGRAL
```
### Output
- 3D predicted structure of the protein.
- Downloadable `.pdb` file.
- Bar chart of amino acid distribution.
- Sample Ramachandran plot.
## Known Limitations
- The application can only predict structures for sequences shorter than **1,500 amino acids** due to the ESMFold API limitations.
- The predictions are based on AI models and should not be used for clinical purposes.
## License
This project is licensed under the MIT License. See the LICENSE file for more details.
## Contact
For questions, feedback, or issues, please contact:
- Abdul Rehman Ikram [[email protected]](mailto:[email protected])