Antigen Specific
Antibody Database

Introduction

AgAb DB (Antigen Specific Antibody Database) is a comprehensive repository supporting computational research in antibody engineering and therapeutic design, with a focus on antibody-antigen interactions. This database addresses the challenge of dispersed binding data by aggregating and standardizing antibody-antigen interaction information from multiple sources.

Data sources

The primary dataset sources creating the database:

• 1. Genbank Database

• 2. SKEMPI 2.0

• 3. Peer-reviewed publications

• 4. Patent datasets

Category Formats present in the database:

Data processing pipeline

• 1. Aggregation: Collection from 14 distinct sources resulting in 25 integrated datasets

• 2. Curation: Multi-stage pipeline combining automated extraction, normalization, and manual verification

• 3. Standardization: Common structure implemented across all studies

• 4. Validation: Automated feasibility checks and manual verification of critical datasets

Data structure

The dataset follows a standardized schema for all studies, containing Antibody-Antigen Pairs along with affinity measures:

Dataset composition

The database includes multiple specialized datasets with diverse characteristics:

• RMNA: Binary binding data for 10 antibodies against 2 antigen targets (RiVax and Apolipoprotein A1),

• BUZZ: Affinity data for Trastuzumab mutations binding to HER2 (524,346 entries)

• DLGO: Examines antibody mutations affecting binding against COVID-19 variants

• AAPT: KD affinity measurements for HER2 VHH (nanobody) mutations.

• AAE: KD binding affinities for VH antibody variants binding to hen egg lysozyme

• AntiBinder: Binary binding data from multiple antibody-antigen pairs.

• COVID-19: Neutralization data for 27,324 SARS-CoV-2 antigen–antibody pairs with full VH/VL sequences (Cov-AbDab).

• HIV: Heavy/light chain antibody sequences targeting HIV (24,004 pairs from LANL database).

• BioMap: Binding ΔG values for 1,706 antigen–antibody complexes across 8 species.

• MET: Affinity data for 4,000 emibetuzumab variants targeting the MET receptor.

• FLAB: Aggregated data from five publications:

• FLAB_Hie2022 (55 datapoints): Binding data for antibodies targeting viral glycoproteins including Ebolavirus glycoprotein, Influenza A hemagglutinin (HA), and its Group A subtype.

• FLAB_Koenig2017 (4,275 datapoints): Extensive binding data for antibodies targeting growth factors such as Vascular Endothelial Growth Factor (VEGF).

• FLAB_Rosace2023 (25 datapoints): Binding data focused on antibodies targeting Tumor Necrosis Factor-alpha (TNF-α) and SARS-CoV spike proteins.

• FLAB_Shanehsazzadeh2023 (445 datapoints): Binding data for antibodies targeting the HER2 receptor, including multiple and zero mutation variants.

• FLAB_Warszawski2019 (2,048 datapoints): Binding data associated with antibodies targeting Hen egg lyzosome.

• Patent databases: Paired antibody-antigen sequences extracted using NLP techniques (113,122 entries spanning 5291 antigens).

• Structure dataset: BBinders extracted from structures in the PDB containing 3969 antigen-antibody pairs.

• ABDesign: Systematic point mutations at binding residues of CDR-H3 (1389 single-point mutants).

• Literature: Semi-manual dataset containing antibodies and antigens extracted from selected research articles containing 5595 curated unique pairs, including 1940 nanobodies.

• AlphaSeq: Dataset involving mutations of antibodies to achieve better binding characteristics across 4 different targets: Human TIGIT, SARS-CoV2_RBD, Human PD-1 and Human HER2 .

• OSH: Affinity binding data using Human NKp30 as a target.

• ABBD: This dataset offers eight antibody-antigen cases enriched through heavy chain mutations.

• Genbank: This dataset offers 413 antigen-antibody pairs derived from the previously published Genbank dataset.

Inclusion criteria

• Transparency and completeness of data

• Relevance to human health

• Quantitative binding affinity measurements

• Complete amino acid sequences for all biomolecules

Citing this work

We make the Therapeutic Antibody Database available as a companion to our paper, that will be posted here once it clears peer review.