README.md

metadata

title: Proteoform Analyzer
emoji: 🧬
colorFrom: indigo
colorTo: green
sdk: gradio
sdk_version: 5.39.0
python_version: '3.11'
app_file: app.py
pinned: false
license: mit
suggested_hardware: zero-a10g
short_description: An AI-powered tool to analyze proteoform effects.

Proteoform Analyzer

An AI-assisted tool to analyze the effects of single-point mutations, post-translational modifications (PTMs), and their pairwise combinations (proteoforms) on proteins of arbitrary oligomeric state (monomers, dimers, tetramers, hexamers, …).

Running on this Space (ZeroGPU)

This Space uses ZeroGPU: a GPU is attached only for the duration of the in-process model calls (ESM2 sequence embedding and the ESM2 zero-shot ddG scorer), which are wrapped with @spaces.GPU in app.py.

What runs here out of the box (CPU/GPU, no extra setup):

• Sequence retrieval, mutation & proteoform enumeration
• ESM2 embeddings + UMAP variant map (GPU-accelerated)
• ESM2 zero-shot ddG stability scores (GPU-accelerated)
• Protein-contact-network (PCN) centralities & communities
• TM-score comparison, impact scoring, and all tables / interactive plots
• 3D structure viewer, including docked receptor+ligand and antibody complexes when those result files are present

What needs extra configuration (degrades cleanly with a message otherwise):

• Boltz-2 folding & docking — set a Space secret BOLTZ_API_KEY (and add boltz-api to requirements.txt) to use the hosted Boltz API. Without a key, mutant/proteoform structures fall back to side-chain grafting onto the WT backbone (TM-score == 1.0 by construction; the app shows a prominent banner explaining this).
• AutoDock Vina docking, Molecular Dynamics, DiffSBDD / GNN ligand design, and RFAntibody antibody design need additional native binaries and/or heavy Python wheels that are not installed on the default Space build.

See DEPLOY_HF_ZEROGPU.md in this repo for the full deployment guide and the "what runs where" matrix, and CHANGES_zerogpu.md for the list of changes made to enable Spaces deployment.

Local use

pip install -r requirements.txt          # lean Space deps, or:
pip install -r proteoform_analyzer/requirements.txt   # full local deps
python -m proteoform_analyzer.gui         # Gradio GUI
python -m proteoform_analyzer.cli --help  # command-line interface