InstaDeepAI/CoVUniBind

CoV-UniBind - Coronavirus Unified Binding Database

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

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.