README.md

metadata

title: BroteinShake BioHub
emoji: 🥤
colorFrom: green
colorTo: gray
sdk: docker
app_port: 7860
pinned: false

BroteinShake

AI-Driven Structural Mimicry & BBB-Shuttle Design

A Gradio application for protein redesign using ProteinMPNN and structural refinement with OpenMM.

Features

1. Sequence Generation: Download PDB structures and generate optimized sequences using ProteinMPNN
2. Structural Refinement: Refine ESM-folded structures with alignment and clash resolution

Usage

1. Enter a PDB ID (e.g., 3kas)
2. Specify fixed chains (to keep unchanged) and variable chains (to redesign)
3. Generate sequences and fold the best design on ESM Atlas
4. Upload the folded structure for refinement

Requirements

• Python 3.10
• Conda environment with OpenMM and PDBFixer
• ProteinMPNN (cloned automatically)

Installation

The space uses conda environment specified in environment.yml.