| --- |
| 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. |
| |
