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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: 34333362
num_examples: 4280
download_size: 4136369
dataset_size: 34333362
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](https://adaptyvbio.com), alongside computational predictions.
Published from <https://proteinbase.com/download>.
```python
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 `v2026-11-01`. Pin it for reproducibility:
```python
ds = load_dataset("adaptyvbio/proteinbase", revision="v2026-11-01")["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"
|