README.md

---
dataset_info:
- config_name: BindingDB_filtered
  features:
  - name: Index 
    dtype: string
  - name: Drug_ID
    dtype: string
  - name: Drug
    dtype: string
  - name: Target_ID
    dtype: string
  - name: Target
    dtype: string
  - name: Y
    dtype: float32
  splits:
  - name: train
    num_examples: 24700
- config_name: CATS
  features:
  - name: Index 
    dtype: string
  - name: Drug
    dtype: string
  - name: IC50
    dtype: float32
  - name: Target
    dtype: string
  - name: Y
    dtype: float32
  splits:
  - name: train
    num_examples: 393
- config_name: HIF2A
  features:
  - name: Index 
    dtype: string
  - name: Y
    dtype: float32
  - name: Drug
    dtype: string
  - name: Target
    dtype: string
  splits:
  - name: train
    num_examples: 37
- config_name: HSP90
  features:
  - name: Index
    dtype: string
  - name: Drug
    dtype: string
  - name: IC50 (nM)
    dtype: float32
  - name: Target
    dtype: string
  - name: Y
    dtype: float32
  splits:
  - name: train
    num_examples: 147
- config_name: LeakyPDB
  features:
  - name: Index 
    dtype: string
  - name: header
    dtype: string
  - name: smiles
    dtype: string
  - name: category
    dtype: string
  - name: seq
    dtype: string
  - name: resolution
    dtype: float32
  - name: date
    dtype: string
  - name: type
    dtype: string
  - name: new_split
    dtype: string
  - name: CL1
    dtype: bool
  - name: CL2
    dtype: bool
  - name: CL3
    dtype: bool
  - name: remove_for_balancing_val
    dtype: bool
  - name: kd/ki
    dtype: string
  - name: value
    dtype: float32
  - name: covalent
    dtype: bool
  splits:
  - name: train
    num_examples: 19443
- config_name: MCL1
  features:
  - name: Index 
    dtype: string
  - name: Y
    dtype: float32
  - name: Drug
    dtype: string
  - name: Target
    dtype: string
  splits:
  - name: train
    num_examples: 25
- config_name: Mpro
  features:
  - name: Index 
    dtype: string
  - name: Drug
    dtype: string
  - name: Y
    dtype: float32
  - name: Target
    dtype: string
  splits:
  - name: train
    num_examples: 2062
- config_name: SYK
  features:
  - name: Index 
    dtype: string
  - name: Y
    dtype: float32
  - name: Drug
    dtype: string
  - name: Target
    dtype: string
  splits:
  - name: train
    num_examples: 44
configs:
- config_name: BindingDB_filtered
  data_files:
  - split: train
    path: BindingDB_filtered/train/data-*
- config_name: CATS
  data_files:
  - split: train
    path: CATS/train/data-*
- config_name: HIF2A
  data_files:
  - split: train
    path: HIF2A/train/data-*
- config_name: HSP90
  data_files:
  - split: train
    path: HSP90/train/data-*
- config_name: LeakyPDB
  data_files:
  - split: train
    path: LeakyPDB/train/data-*
- config_name: MCL1
  data_files:
  - split: train
    path: MCL1/train/data-*
- config_name: Mpro
  data_files:
  - split: train
    path: Mpro/train/data-*
- config_name: SYK
  data_files:
  - split: train
    path: SYK/train/data-*
license: cc-by-4.0
pretty_name: BALM-Benchmark
tags:
  - chemistry
  - biology
size_categories:
  - 10K<n<100K
---

# Dataset Card for BALM-Benchmark

<!-- Provide a quick summary of the dataset. -->

BALM-Benchmark is a comprehensive benchmark suite that combines multiple seminal binding affinity prediction datasets in one place.
...

## Dataset Details

### Dataset Description

<!-- Provide a longer summary of what this dataset is. -->

- **Dataset Repository:** https://huggingface.co/datasets/BALM/BALM-benchmark
- **Code Repository:** https://github.com/meyresearch/BALM
- **Paper:** TBA
- **Language(s) (NLP):** English
- **License:** CC-BY-4.0

### Dataset Columns

- **BindingDB_filtered**:
    - **Index** (`string`): Index of the ligand-target pair.
    - **Drug_ID** (`string`): Index of the ligand from the TDC.
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **Target_ID** (`string`): Index of the target protein from the TDC.
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
    - **Y** (`float32`): binding affinity value in pKd.
- **CATS**: 
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **IC50** (`float32`): binding affinity value in IC50. 
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
    - **Y** (`float32`): binding affinity value in pKd.
- **HIF2A**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Y** (`float32`): binding affinity value in pKd.
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
- **HSP90**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **IC50 (nM)** (`float32`): binding affinity value in IC50. 
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
    - **Y** (`float32`): binding affinity value in pKd.
- **LeakyPDB**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **header** (`string`): TBA 
    - **smiles** (`string`): TBA 
    - **category** (`string`): TBA 
    - **seq** (`string`): TBA 
    - **resolution** (`float32`): TBA 
    - **date** (`string`): TBA 
    - **type** (`string`): TBA 
    - **new_split** (`string`): TBA 
    - **CL1** (`bool`): TBA 
    - **CL2** (`bool`): TBA 
    - **CL3** (`bool`): TBA 
    - **remove_for_balancing_val** (`bool`): TBA 
    - **kd/ki** (`string`): TBA 
    - **value** (`float32`): TBA 
    - **covalent** (`bool`): TBA 
- **MCL1**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Y** (`float32`): binding affinity value in pKd.
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
- **Mpro**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Y** (`float32`): binding affinity value in pKd.
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).
- **SYK**:
    - **Index** (`string`): Index of the ligand-target pair. 
    - **Y** (`float32`): binding affinity value in pKd.
    - **Drug** (`string`): Ligand sequence (i.e., SMILES string).
    - **Target** (`string`): Protein sequence (i.e., sequence of amino acids).


### Dataset Sources

- **BindingDB_filtered**:
- **CATS**: 
- **HIF2A**:
- **HSP90**:
- **LeakyPDB**:
- **MCL1**:
- **Mpro**:
- **SYK**:

## Uses

BALM-Benchmark was initially created as a part of the BALM project (https://github.com/meyresearch/BALM) which fine-tunes Protein and Ligand Language Models by optimizing the distance between protein and ligand embeddings in a shared space using the cosine similarity metric that directly represents experimental binding affinity.
Nevertheless, BALM-Benchmark can be used by itself, just like any other HuggingFace dataset:

```python
from datasets import load_dataset

# For instance, you want to load SYK data. Change the second argument into SYK
syk_data = load_dataset("BALM/BALM-benchmark", "SYK", split="train")
```

As mentioned in the [Dataset Sources](#dataset-sources), the available datasets are:

- `BindingDB_filtered`
- `CATS`
- `HIF2A`
- `HSP90`
- `LeakyPDB`
- `MCL1`
- `Mpro`
- `SYK`

Notice that all datasets only have one split (`train`). This is intentional such that the users can define their own splits, and can experiment with more random seeds for robustness.
We highly recommend checking out different strategies for splitting the data (e.g., BindingDB) in [our BALM code repository](https://github.com/meyresearch/BALM/blob/refactor/balm/datasets/bindingdb_filtered.py#L157-L169).

## Citation

<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->

**BibTeX:**

```
In preparation
```

## Dataset Card Contact

- Rohan Gorantla ([email protected])
- Aryo Pradipta Gema ([email protected])
- Antonia Mey ([email protected])