nativeready 0.4.0

Python SDK for the NativeReady API: predict native mass spectrometry suitability from a protein sequence.

nativeready

Python SDK for the NativeReady API. Predict whether a protein sequence is likely to give usable native mass spectrometry data, in seconds.

pip install nativeready

Quick start

from nativeready import predict

result = predict("MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG")
print(result)
# PredictionResult(score=97, label='Excellent', ci=[88-100], model='0.4-esm2-glyco-tm')

print(result.score)         # 97
print(result.label)         # 'Excellent'
print(result.is_ood)        # False
print(result.recommendations)

Common use cases

Predict from a FASTA file

from nativeready import Client

client = Client()
results = client.predict_fasta("my_proteins.fasta")
for r in results:
    print(r.uniprot_id, r.score, r.label)

Predict from a UniProt accession

from nativeready import Client

client = Client()
result = client.predict_uniprot("P00918")  # Carbonic anhydrase 2
print(result.score, result.label)

Batch prediction with progress bar

from nativeready import Client

client = Client()
sequences = [
    {"id": "ubiquitin", "sequence": "MQIFVKTLTGKTITLEV..."},
    {"id": "lysozyme",  "sequence": "KVFGRCELAAAMKR..."},
    "MSHHWGYGKHNGPEHWHKDF...",  # raw string also works
]
results = client.predict_batch(sequences)  # tqdm progress bar if installed

Pandas DataFrame output (with pandas extra)

pip install nativeready[pandas]

import pandas as pd
from nativeready import Client

client = Client()
results = client.predict_fasta("my_proteins.fasta")
df = pd.DataFrame([r.as_dict() for r in results])
df.to_csv("results.csv", index=False)

Command line interface

The package installs a nativeready CLI:

# Single sequence
nativeready predict --sequence "MQIFVKTLTGKTITLEV..."

# UniProt accession
nativeready predict --uniprot P00918

# Multiple UniProt accessions (comma-separated)
nativeready predict --uniprot P00918,P0CG48,P00698

# FASTA file with CSV output
nativeready predict --fasta proteins.fasta --output results.csv

# FASTA file with JSON output
nativeready predict --fasta proteins.fasta --output results.json

# Health check
nativeready health

# Public feedback statistics
nativeready stats

What the predictions mean

Each PredictionResult contains:

• score — calibrated suitability score, 0 to 100
• label — Excellent (>= 80), Good (>= 65), Fair (>= 50), Poor (>= 35), Unsuitable (< 35)
• confidence_lower, confidence_upper — 95 percent confidence interval (wider when out-of-distribution)
• is_ood — True if the sequence is unusual relative to training data; trust the score with extra caution
• risk_factors — per-feature risk levels (length, MW, hydrophobicity, pI, instability, cysteine content)
• recommendations — buffer choice, sample-prep guidance, and instrument-mode notes
• model_version — server-side model identifier (e.g., 0.4-esm2-glyco-tm)

API server

By default the SDK calls https://nativeready-production.up.railway.app. To use a self-hosted or local deployment:

from nativeready import Client
client = Client(base_url="http://localhost:8000")

Honest scope

NativeReady is currently most reliable as a positive-suitability triage tool, not a validated failure detector. With only two evidence-based real-failure records in the training set, the negative-class performance is not yet statistically meaningful. High-confidence positive predictions can be trusted; low-confidence predictions should be treated as a flag for manual review, not a verdict. See the bioRxiv preprint for full methodology and limitations.

Citing

Znabu BFZ, Atif Z. NativeReady: an open benchmark and sequence-based triage
model for native mass spectrometry suitability. bioRxiv, 2026.
https://doi.org/10.64898/2026.05.03.722506

License

MIT. See LICENSE.

Links

• API server source: https://github.com/brhanufen/nativeready
• Web tool: https://nativeready.netlify.app
• Open dataset (634 proteins, CC-BY 4.0): in the data/ folder of the main repository
• Issues: https://github.com/brhanufen/nativeready/issues