Benchmarking antibody clustering methods using sequence, structural, and machine learning similarity measures for antibody discovery applications

AbSet: A Standardized Data Set of Antibody Structures for Machine Learning Applications

Machine learning algorithms have played a fundamental role in the development of therapeutic antibodies by being trained on data sets of sequences and/or structures. However, structural data sets remain limited, especially those that include antibody-antigen complexes. Additionally, many of the available structures are not standardized, and antibody-specific databases often do not provide molecular descriptors that could enhance ML models. To address this gap, we introduce AbSet, a curated dataset comprising over 800,000 antibody structures and corresponding molecular descriptors, including both experimentally determined and in silico-generated antibody-antigen complexes. We systematically retrieved antibody structures from the Protein Data Bank (PDB), applied rigorous standardization protocols, and expanded the dataset through large-scale protein-protein docking to generate structural variants of antibody-antigen interactions. Each model was classified as high, medium, acceptable, or incorrect quality based on structural similarity to reference experimental complexes. This classification enables both the construction of a decoy set of confirmed non-binders and the generation of high-confidence augmented structural data for machine learning applications. AbSet is publicly available via the Zenodo repository, with accompanying scripts hosted on GitHub (https://github.com/SFBBGroup/AbSet.git).

Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data

Repertoire sequencing allows us to investigate the antibody-mediated immune response. The clustering of sequences is a crucial step in the data analysis pipeline, aiding in the identification of functionally related antibodies. The conventional clustering approach of clonotyping relies on sequence information, particularly CDRH3 sequence identity and V/J gene usage, to group sequences into clonotypes. It has been suggested that the limitations of sequence-based approaches to identify sequence-dissimilar but functionally converged antibodies can be overcome by using structure information to group antibodies. Recent advances have made structure-based methods feasible on a repertoire level. However, so far, their performance has only been evaluated on single-antigen sets of antibodies. A comprehensive comparison of the benefits and limitations of structure-based tools on realistic and diverse repertoire data is missing. Here, we aim to explore the promise of structure-based clustering algorithms to replace or augment the standard sequence-based approach, specifically by identifying low-sequence identity groups. Two methods, SAAB+ and SPACE2, are evaluated against clonotyping. We curated a dataset of well-annotated pairs of antibodies that show high overlap in epitope residues and thus bind the same region within their respective antigen. This set of antibodies was introduced into a simulated repertoire to compare the performance of clustering approaches on a diverse antibody set. Our analysis reveals that structure-based methods do group more antibodies together compared to clonotyping. However, it also highlights the limitations associated with the need for same-length CDR regions by SPACE2. This work thoroughly compares the utility of different clustering methods and provides insights into what further steps are required to effectively use antibody structural information to group immune repertoire data.

RIOT-Rapid Immunoglobulin Overview Tool-annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database

Antibodies are a cornerstone of the immune system, playing a pivotal role in identifying and neutralizing infections caused by bacteria, viruses, and other pathogens. Understanding their structure, and function, can provide insights into both the body's natural defenses and the principles behind many therapeutic interventions, including vaccines and antibody-based drugs. The analysis and annotation of antibody sequences, including the identification of variable, diversity, joining, and constant genes, as well as the delineation of framework regions and complementarity-determining regions, is essential for understanding their structure and function. Currently analyzing large volumes of antibody sequences is routine in antibody discovery, requiring fast and accurate tools. While there are existing tools designed for the annotation and numbering of antibody sequences, they often have limitations such as being restricted to either nucleotide or amino acid sequences; slow execution times; or reliance on germline databases that are closed, frequently changed, or have sparse coverage for some species. Here, we present the Rapid Immunoglobulin Overview Tool (RIOT), a novel open-source solution for antibody numbering that addresses these shortcomings. RIOT handles nucleotide and amino acid sequence processing, comes integrated with an Open Germline Receptor Database, and is computationally efficient. We hope that the tool will facilitate rapid annotation of antibody sequencing outputs for the benefit of understanding antibody biology and discovering novel therapeutics.

Large-scale data mining of four billion human antibody variable regions reveals convergence between therapeutic and natural antibodies that constrains search space for biologics drug discovery

The naïve human antibody repertoire has theoretical access to an estimated > 1015 antibodies. Identifying subsets of this prohibitively large space where therapeutically relevant antibodies may be found is useful for development of these agents. It was previously demonstrated that, despite the immense sequence space, different individuals can produce the same antibodies. It was also shown that therapeutic antibodies, which typically follow seemingly unnatural development processes, can arise independently naturally. To check for biases in how the sequence space is explored, we data mined public repositories to identify 220 bioprojects with a combined seven billion reads. Of these, we created a subset of human bioprojects that we make available as the AbNGS database (https://naturalantibody.com/ngs/). AbNGS contains 135 bioprojects with four billion productive human heavy variable region sequences and 385 million unique complementarity-determining region (CDR)-H3s. We find that 270,000 (0.07% of 385 million) unique CDR-H3s are highly public in that they occur in at least five of 135 bioprojects. Of 700 unique therapeutic CDR-H3, a total of 6% has direct matches in the small set of 270,000. This observation extends to a match between CDR-H3 and V-gene call as well. Thus, the subspace of shared ('public') CDR-H3s shows utility for serving as a starting point for therapeutic antibody design.