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ESMFold Protein Structure Predictor

ESMFold Protein Structure Predictor

Overview

The ESMFold Protein Structure Predictor is a web application that uses the ESM-2 language model to predict the 3D structure of proteins based on their amino acid sequences. This tool allows users to input protein sequences in text format or upload a FASTA file and visualize the predicted protein structure in 3D. It also provides pLDDT scores, which are confidence measures for the predicted structure.

Features

  • Protein Sequence Input: Accepts protein sequences via text input or FASTA file upload.
  • Structure Prediction: Predicts protein structures using the ESMFold API.
  • 3D Visualization: Visualizes the predicted protein structure using Py3Dmol.
  • pLDDT Scores: Extracts and displays pLDDT scores, indicating the confidence of the predicted structure.
  • Download Option: Allows users to download the predicted PDB file.

Requirements

  • Python 3.7 or higher
  • Streamlit
  • Requests
  • Urllib3
  • Py3Dmol

Installation

  1. Clone the repository: 
    git clone https://github.com/yourusername/esmfold-predictor.git
cd esmfold-predictor
  2. Create and activate a virtual environment: 
    python3 -m venv venv
source venv/bin/activate  # On Windows, use `venv\Scripts\activate`
  3. Install the required packages: 
    pip install -r requirements.txt

Usage

  1. Run the Streamlit application: 
    streamlit run esm.py
  2. Open your web browser and navigate to http://localhost:8501.