Datasets:

SupraBench
/

Binding-Affinity

---
license: cc-by-4.0
task_categories:
- tabular-regression
tags:
- chemistry
- supramolecular
- binding-affinity
- host-guest
- smiles
- molecular-structures
pretty_name: SupraBench Binding Affinity (Comprehensive Anchor)
size_categories:
- 1K<n<10K
configs:
- config_name: default
  data_files:
  - split: train
    path: data/records.parquet
---

# SupraBench Binding Affinity — Comprehensive Anchor Dataset

- 📄 **Paper:** [`arXiv:2606.13477`](https://arxiv.org/abs/2606.13477)
- 💻 **Code:** https://github.com/Tianyi-Billy-Ma/SupraBench

Each row is a host–guest **binding-affinity record** from SupraBench, enriched with
full molecular-structure data for **both** the host and the guest (SMILES, a 2D
depiction, and a 3D conformer) plus the **experimental environment** (solvent,
temperature, pH). It is the structure-complete companion to the
[`SupraBench/bap`](https://huggingface.co/datasets/SupraBench/bap) task split.

## Contents

| | count |
|---|---|
| Binding records (rows) | 2,609 |
| of which CB[7] supplement | 217 |
| host SMILES present | 2,386 (91%) |
| guest SMILES present | 2,605 (100%) |
| host 3D conformer present | 2,340 |
| guest 3D conformer present | 2,528 |
| environment (solvent) present | 2,539 |

Every record is kept; fields are left **empty** where the corresponding structure
or environment value was unavailable (e.g., exotic synthetic hosts with no public
structure). 2D depictions are embedded inline; 3D conformers ship as repo files.

## Schema

| column | type | notes |
|---|---|---|
| `task_id` | string | record id (`t1_<interaction_id>`; `\|`-joined ids are averaged measurements) |
| `host_name` | string | host molecule name |
| `host_smiles` | string | host canonical SMILES (empty if unresolved) |
| `host_image_2d` | Image | host 2D depiction (empty if unresolved) |
| `host_3d_basename` | string | host 3D file basename -> `structures_3d/<base>.{xyz,sdf,pdb}` |
| `guest_name` | string | guest molecule name |
| `guest_smiles` | string | guest canonical SMILES |
| `guest_image_2d` | Image | guest 2D depiction |
| `guest_3d_basename` | string | guest 3D file basename |
| `binding_affinity` | float64 | log K_a |
| `solvent` | string | measurement solvent |
| `temperature` | string | measurement temperature (e.g., `25.0C`) |
| `ph` | string | measurement pH |
| `source` | string | `eupmc` (SupraBank/Europe PMC pipeline) or `cb7_supplement` |

## 3D structures

3D conformers (RDKit ETKDGv3 + MMFF94/UFF) are shipped as repo files under
`structures_3d/`, one `.xyz`, `.sdf`, and `.pdb` per molecule, named by InChIKey
(1,399 molecules x 3 formats = 4,197 files).

> **Note.** The 3D files are **not shown in the dataset viewer** (XYZ/SDF/PDB are
> not a HuggingFace column type). They live under the **Files and versions** tab.
> Each record links to them through the `host_3d_basename` and `guest_3d_basename`
> columns, where the file path is `structures_3d/<basename>.{xyz,sdf,pdb}`.

Download a record's 3D structures programmatically:

```python
from datasets import load_dataset
from huggingface_hub import hf_hub_download

ds = load_dataset("SupraBench/Binding-Affinity", split="train")
row = ds[0]

# host conformer (XYZ); swap the extension for .sdf or .pdb
host_xyz = hf_hub_download(
    repo_id="SupraBench/Binding-Affinity", repo_type="dataset",
    filename=f"structures_3d/{row['host_3d_basename']}.xyz",
)
guest_sdf = hf_hub_download(
    repo_id="SupraBench/Binding-Affinity", repo_type="dataset",
    filename=f"structures_3d/{row['guest_3d_basename']}.sdf",
)
```

An empty `host_3d_basename` / `guest_3d_basename` means no 3D conformer is
available for that molecule (see *Known limitations* and `failures.csv`).

## Resolution & validation

SMILES were resolved through a cascade (local SupraBank/CB7 dictionaries -> InChI
-> the record's prompt text -> PubChem by CID/name -> OPSIN -> the SupraBank
molecule catalog via exact-name match). Every resolved SMILES passes RDKit
parsing; host families (cucurbiturils, sulfonatocalixarenes, calixarenes)
additionally pass a chemistry sanity gate (atom/ring/charge counts must match the
name). 3D conformers are geometry-validated (no atom clashes / degenerate
embeddings). Components that failed the gate, framework materials (zeolites),
proteins, and supramolecular assemblies (rotaxanes) are left with empty structure
fields; the per-molecule status is in `failures.csv`.

### Known limitations
- Stereoisomer pairs (cis/trans, R/S, L/D, anti/syn) may share a flattened 2D
  skeleton because the source SMILES lack stereo descriptors.
- `\|`-joined `task_id`s are averaged over multiple raw measurements; the
  reported environment is taken from the first underlying interaction.

## Sources & license

Derived from [SupraBank](https://suprabank.org/) (CC-BY-4.0),
[PubChem](https://pubchem.ncbi.nlm.nih.gov/), and
[OPSIN](https://github.com/dan2097/opsin). Released under CC-BY-4.0.