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babilonczyk/protein-similarity-api

sourceHugging Faceupdated 1y agoView on Hugging Face

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App README

protein-similarity-api

A lightweight, production-ready FastAPI service for comparing protein sequences using state-of-the-art transformer embeddings (ESM-2).

It provides a simple REST API to measure semantic similarity between protein sequences, returning a similarity score based on cosine distance in embedding space.

Why this matters?

Protein similarity is at the heart of functional annotation, homology detection, and structure prediction. This API lets anyone (researcher, student, dev) compare protein sequences using powerful models.

Features

—Compare two protein sequences using ESM-2
—Returns cosine similarity + classification (homologous vs. non-homologous)
—Lightweight, deployable on free-tier platforms like Render or Railway
—Clean FastAPI structure, easy to extend (e.g. embeddings endpoint, caching)

API Endpoints

`POST /compare`

Compare two sequences and get similarity:

Request:

json

{
  "sequence_1": "MSSKVIFF...",
  "sequence_2": "MTTRLIFF...",
  "model": "esm_2_650m"
}

Response:

json

{
  "cosine_similarity": 0.57,
  "classification": "moderate similarity (possible remote homolog)",
  "model": "ESM-2 650M"
}

How to run it?

shell

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

uvicorn main:app --reload