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.