Datasets:

adaptyvbio
/

proteinbase

license: odc-by
dataset_info:
  features:
    - name: id
      dtype: string
    - name: name
      dtype: string
    - name: sequence
      dtype: string
    - name: author
      dtype: string
    - name: designMethod
      dtype: string
    - name: evaluations
      list:
        - name: type
          dtype: string
        - name: metric
          dtype: string
        - name: valueType
          dtype: string
        - name: unit
          dtype: string
        - name: value
          dtype: string
        - name: target
          dtype: string
        - name: method
          dtype: string
        - name: measuredAt
          dtype: string
  splits:
    - name: proteins
      num_bytes: 30683901
      num_examples: 4069
  download_size: 3703301
  dataset_size: 30683901
configs:
  - config_name: default
    data_files:
      - split: proteins
        path: data/proteins-*
size_categories:
  - 1K<n<10K
pretty_name: Proteinbase
tags:
  - biology
  - proteins
  - protein-binding
  - ppi

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"