|
|
--- |
|
|
tags: |
|
|
- antibody |
|
|
- antigen |
|
|
- binding |
|
|
- COVID-19 |
|
|
- SARS-CoV-2 |
|
|
- benchmark |
|
|
pretty_name: CoV-UniBind |
|
|
--- |
|
|
<div align="center"> |
|
|
|
|
|
<h1>CoV-UniBind - Coronavirus Unified Binding Database</h1> |
|
|
|
|
|
</div> |
|
|
|
|
|
<p align="center"> |
|
|
<img src="https://cdn-uploads.huggingface.co/production/uploads/681b661257cfafb5ead152d1/WvLoDuemHIwY8bQfOMahb.png" alt="Description" width="300"/> |
|
|
</p> |
|
|
|
|
|
**CoV-UniBind** curates and integrates structural and biochemical data on antibodies specifically elicited by SARS-CoV-2 and |
|
|
related coronaviruses. It links 3D antibody structures to their binding properties across viral variants, incorporating |
|
|
epitope and sequence information. This dataset serves as a comprehensive resource for analysing antibody-antigen |
|
|
interactions in the context of COVID-19 and provides a foundation for binding classification and regression tasks using |
|
|
deep learning models. |
|
|
|
|
|
## Database Overview |
|
|
|
|
|
| Dataset | Description | Label | Type | References (doi) | |
|
|
|------|-------------|-------|-----| ------- | |
|
|
| covabdab | Binding labels from the Coronavirus Antibody Database (CoV-AbDab) | binding | bool | 10.1093/bioinformatics/btaa739 | |
|
|
| dms_bloom | Deep Mutational Scanning escape data from Greaney et al. 2022 | escape | float | 10.1038/s41564-021-00972-2; 10.1016/j.chom.2020.11.007; 10.1038/s41467-021-24435-8; 10.1016/j.xcrm.2021.100255; 10.1126/science.abf9302; 10.1038/s41467-021-24435-8; 10.1038/s41564-021-00972-2; 10.1038/s41586-021-04385-3; 10.1038/s41586-022-04980-y; 10.1038/s41586-021-03817-4; 10.1038/s41586-021-03807-6 | |
|
|
| dms_cao | Deep Mutational Scanning escape data from Cao et al. 2023 | escape | float | 10.1038/s41586-022-05644-7 | |
|
|
| jian_elisa | ELISA antibody IC50 measurements from Jian et al. 2025 | IC50 | float | 10.1038/s41586-024-08315-x | |
|
|
| spr | Surface Plasmon Resonance antibody affinity measurements from multiple sources | KD | float | 10.1038/s41467-024-54916-5; 10.1038/s41586-020-2380-z; 10.1038/s41467-021-24514-w; 10.1016/j.immuni.2022.06.005; 10.1016/j.xcrm.2023.100991 | |
|
|
| drdb | Neutralisation potency data from the SARS-CoV-2 Resistance Database (DRDB) | IC50 | float | 10.1371/journal.pone.0261045 | |
|
|
|
|
|
## Database Structure |
|
|
``` |
|
|
. |
|
|
├── antibody_info |
|
|
│ └── antibody_synonyms.csv |
|
|
├── data |
|
|
│ ├── covabdab_binding.parquet |
|
|
│ │ └── structures |
|
|
│ │ ├── processed.zip |
|
|
│ │ └── trimmed.zip |
|
|
│ ├── dms_bloom_ab_escape.parquet |
|
|
│ ├── dms_cao_ab_escape.parquet |
|
|
│ ├── drdb_binding_potency.parquet |
|
|
│ ├── jian_elisa_ab_ic50.parquet |
|
|
│ └── spr_ab_affinity.parquet |
|
|
├── scores |
|
|
│ ├── covabdab_binding_scores.parquet |
|
|
│ ├── dms_bloom_ab_escape_scores.parquet |
|
|
│ ├── dms_cao_ab_escape_scores.parquet |
|
|
│ ├── drdb_binding_potency_scores.parquet |
|
|
│ ├── jian_elisa_ab_ic50_scores.parquet |
|
|
│ └── spr_ab_affinity_scores.parquet |
|
|
├── cov-unibind.py |
|
|
└── README.md |
|
|
``` |
|
|
|
|
|
## Usage Guide |
|
|
|
|
|
```python |
|
|
from datasets import load_dataset |
|
|
|
|
|
data='drbd' # specify the dataset name based on table above |
|
|
|
|
|
dataset = load_dataset("InstaDeepAI/cov-unibind",name=data) |
|
|
``` |
|
|
|
|
|
|
|
|
## Dataset Schema |
|
|
|
|
|
The table below includes information about the columns contained in the datasets. |
|
|
|
|
|
| Column Name | Description | Type | Nullable | Example | |
|
|
|---|---|---|---|---| |
|
|
| `antibody_name` | Name of the antibody | *str* | False | `bd30_515;bd_515` | |
|
|
| `antigen_lineage` | Antigen lineage | *str* | False | `BA.1` | |
|
|
| `target_value` | Experimental binding value| *float* or *bool* | False | `-2.327902` or `True` | |
|
|
| `target_type` | Type of target value | *str* | False | `IC50_log10_fold` | |
|
|
| `source_name` | Source of the data | *str* | False | `jian_2024_nature` | |
|
|
| `source_doi` | DOI of the source | *str* | False | `10.1038/s41586-024-08315-x` | |
|
|
| `assay_name` | Name of the assay | *str* | False | `elisa` | |
|
|
| `pdb_id` | PDB structure ID | *str* | False | `7e88` | |
|
|
| `structure_release_date` | Release date of the structure | *str* | False | `03/01/21` | |
|
|
| `structure_resolution` | Resolution of the structure (Å) | *float* | False | `3.14` | |
|
|
| `mutations` | Lineage consensus mutations | *str* | False | `A67V H69- V70- T95I...` | |
|
|
| `antigen_chain_ids` | Chain IDs of the antigen | *str* | False | `C` | |
|
|
| `antigen_domain` | Domain of the antigen | *str* | False | `RBD` | |
|
|
| `antigen_residue_indices` | Residue indices of the antigen | *str* | False | `(13, 568)` | |
|
|
| `antigen_residue_indices_trimmed` | Antigen residue indices, trimmed | *float* | True | `(333, 526)` | |
|
|
| `antigen_host` | Host organism of the antigen | *str* | False | `severe acute respiratory syndrome coronavirus 2 (2697049)` | |
|
|
| `antibody_heavy_chain_id` | Heavy chain ID of the antibody | *str* | False | `C` | |
|
|
| `antibody_light_chain_id` | Light chain ID of the antibody | *str* | False | `B` | |
|
|
| `epitope_residues` | Residues of the epitope | *str* | False | `R403 D405 T415` | |
|
|
| `epitope_mutations` | PDB antigen mutations in the epitope | *str* | True | `D405T` | |
|
|
| `epitope_domain` | Spike domain where the antibody binds | *str* | False | `RBD` | |
|
|
| `epitope_alteration_count` | Number of alterations in the epitope | *float* | True | `2` | |
|
|
| `spike_sequence` | Full spike protein sequence | *str* | False | `MFVFLVLLPLVSSQCVNLTTRTQL...` | |
|
|
| `antibody_heavy_chain_sequence` | Sequence of the antibody heavy chain | *str* | False | `EVQLVESGGGLVQPGGSLRLSCAASEFIVSRNYMSWVR...` | |
|
|
| `antibody_light_chain_sequence` | Sequence of the antibody light chain | *str* | False | `DIQMTQSPSSLSASVGDRVTITCQASQDINKYLNWYQQK...` | |
|
|
| `antibody_vh_sequence` | Sequence of the VH domain | *str* | False | `EVQLVESGGGLVQPGGSLRLSCAASEFIVSRNYMSWVRQ...` | |
|
|
| `antibody_vl_sequence` | Sequence of the VL domain | *str* | False | `DIQMTQSPSSLSASVGDRVTITCQASQDINKYLNW...` | |
|
|
| `antigen_sequence` | Full antigen sequence | *str* | False | `TNLCPFDEVF-NATRFASVYAWNR--KRISNCVADYSVLYNLAPFFTFKCYGVSP...` | |
|
|
| `antigen_sequence_trimmed` | Trimmed antigen sequence | *float* | True | `TRFASV-YAWNRKRISNCVADYSVLYNLAPFFT-FKCYGVSP...` | |
|
|
| `antigen_sequence_without_indels`| Antigen sequence without insertions/deletions | *str* | False | `TNLCPFDEVFNATRFASVYAWNRKRISNCVAD...` | |
|
|
| `antigen_sequence_trimmed_without_indels` | Trimmed antigen sequence without insertions/deletions | *float* | True | `NATRFASVYAWNRKRISNCVAD...` | |
|
|
| `antigen_pdb_sequence` | Antigen sequence from PDB | *str* | False | `TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSA...` | |
|
|
| `antigen_pdb_sequence_trimmed` | Trimmed antigen sequence from PDB | *float* | True | `NATRFASVYAWNRKRISNCVADYSVLYNSA...` | |
|
|
|
|
|
## Acknowledgments |
|
|
|
|
|
This project makes use of publicly available antibody datasets listed above. We acknowledge the contributions by the teams |
|
|
responsible for compiling and maintaining these valuable resources. |
|
|
|
