| --- |
| 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](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 `v2026-10-12`. Pin it for reproducibility: |
|
|
| ```python |
| 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" |
|
|
