Proteinbase

Experimentally validated protein-protein interaction data from Adaptyv Bio, alongside computational predictions. Published from https://proteinbase.com/download.

from datasets import load_dataset

ds = load_dataset("adaptyvbio/proteinbase")["proteins"]

for ev in ds[0]["evaluations"]:
    print(ev["metric"], ev["method"], ev["value"], ev["unit"])

This is one unpartitioned corpus, so there is a single split named proteins rather than the usual train/test division.

This snapshot is tagged v2026-10-12. Pin it for reproducibility:

ds = load_dataset("adaptyvbio/proteinbase", revision="v2026-10-12")["proteins"]

Columns

Column	Description
id	Stable protein identifier, safe to treat as a primary key.
name	Optional reference label; empty if none was supplied.
sequence	Amino-acid sequence.
author	Creator handle when available.
designMethod	Slug of the design pipeline that generated the protein.
evaluations	List of measurements for this protein (see below).

evaluations

Field	Description
type	computational, experimental, or curated.
metric	Metric slug, e.g. kd, tm-score, expressed.
target	Binding target slug when applicable, otherwise empty.
valueType	Parse hint: numeric, boolean, label, or json.
unit	Unit symbol such as nM; empty when the metric is unitless.
value	The measurement, encoded as a string (see note).
method	Tool or protocol that produced it: esmfold, boltz2, bli, spr.
measuredAt	ISO timestamp of the evaluation.

value is always a string. It is a union of number, boolean, label, and structured JSON in the source data, and Arrow has no union type. Parse it according to valueType: numeric with float(), boolean against "true"/"false", json with json.loads(), label as-is.

When the same metric appears more than once

Computational entries are deduplicated: where a tool has been run more than once for the same protein and metric, only the most recent result is included.

Experimental entries are not deduplicated. Several entries sharing a metric and method are genuine replicate measurements and should be aggregated (e.g. averaged) rather than treated as duplicates.

Entries sharing a metric but differing in method are different tools measuring the same quantity, and are never merged.

License

Open Data Commons Attribution License (ODC-By). Include this text in any work building on Proteinbase:

"This work used Proteinbase by Adaptyv Bio under ODC-BY license"