This review compiles the data resources related to polyreactive antibodies and places a particular emphasis on computational models for predicting antibody polyreactivity, which includes empirical models based on physicochemical properties, traditional machine learning models, deep learning networks, and protein language models.
Abstract
Antibody polyreactivity refers to the ability of a monoclonal antibody to non-specifically bind to a diverse range of antigens. While this property may be an intrinsic mechanism of the immune response, it poses significant challenges in therapeutic antibody development, often leading to off-target effects, poor pharmacokinetics, and potential toxicity. This review compiles the data resources related to polyreactive antibodies and places a particular emphasis on computational models for predicting antibody polyreactivity. The latter includes empirical models based on physicochemical properties, traditional machine learning models, deep learning networks, and protein language models. Through delineating the complexity of antibody polyreactivity, this review emphasizes the critical role and growing potential of computational prediction tools in selecting and engineering antibody drug candidates at early stages, thereby reducing development risks and accelerating the development of safer and better therapeutic antibodies.
This thesis examines the integration of machine learning into computational structural biology, with an emphasis on modelling and predicting antibody–antigen interactions. Such interactions are fundamental to numerous biological processes and are central to therapeutic antibody design. Despite recent advances in AI-based protein structure prediction, antibodies remain particularly challenging targets due to the high variability of their complementarity-determining regions, the limited availability of experimental structures, and the lack of strong co-evolutionary signal.
To address these challenges, this work introduces several methodological contributions. In Chapter 2,DeepRank-GNN-esm incorporates embeddings from protein language models to replace computationally expensive evolutionary features, thereby improving both predictive performance and efficiency in scoring protein–protein complexes. In Chapter 3, a modelling pipeline is introduced that employs a flow-matching algorithm to effectively sample the conformational diversity of the antibody CDR-H3 loop. When integrated with ensemble docking, this approach significantly improves the accuracy of antibody–antigen complex modelling compared to existing methods. In Chapter 4, the thesis presents AbTune, a sequence-specific fine-tuning strategy for protein language models that enhances predictive performance across multiple antibody-related tasks, including structure prediction, mutation effect estimation, and binding affinity prediction, while remaining computationally efficient. In Chapter 5, DeepRank-Ab is developed as a geometric deep learning-based scoring function tailored to antibody–antigen complexes, achieving state-of-the-art performance in ranking near-native docking conformations. Chapter 6 summarizes the main findings of the thesis and discusses future research directions.
Collectively, these contributions demonstrate how machine learning can be applied to address key limitations in antibody modelling and to facilitate the rational design of antibody-based therapeutics.
This work designs a biological prior-guided feature fusion framework that integrates pseudo-structural epitope knowledge and CDR-specific attention mechanisms via a mixture-of-experts architecture to effectively capture complex binding landscapes in antibody screening and drug residence time analysis.
G. Luo, Junkai Wang, Sizhe Zhang et al.· Bioinformatics· 0 citations
Determining the structural basis of antigen recognition by antibodies and T cell receptors (TCRs) provides critical insights into effective immune targeting and can inform design of biotherapeutics and vaccines. Accurate computational modeling of antibodies and TCRs in complex with their targets poses a major challenge for predictive methods, including AlphaFold, which is generally accurate for modeling protein complexes but has shown limited success for immune recognition. In this study we assessed the performance of AlphaFold2, AlphaFold3, increased sampling protocols, and related deep learning methods for modeling antibody-protein, antibody-peptide, and TCR-peptide-major histocompatibility complex (pMHC) recognition. We show that increased sampling and AlphaFold3 generally improve performance relative to default sampling and AlphaFold2, however predictive accuracy and improvement levels varied considerably among interface classes, with antibody-peptide complexes representing a challenge despite their small antigen size. Comparing per-case success across methods showed some complementarity, indicating opportunities for increased success through model pooling approaches, for instance increasing antibody-peptide near-native success from 41% to 59%. Analysis of AlphaFold confidence scores and modeling of a noncanonical complex provided further insights into predictive performance. These results highlight considerations for predictive antibody and TCR complex modeling efforts, while revealing key distinctions among protocols, scoring, and immune complex classes.
Rui Yin, S. Saravanakumar, Shu Yuan Shi et al.· bioRxiv· 0 citations
CLDN18.2 is a promising tumor-specific antigen; however, the development of therapeutic antibodies against it is challenged by the need for simultaneous optimization of affinity and developability. To address this, we present cdrGPT, a deep learning framework based on GPT-2 for de novo generation of complementarity-determining region H3 (CDRH3) sequences. Our approach integrates pre-training on the Observed Antibody Space (OAS) database with structural templating derived from the known antibody zolbetuximab. Generated sequences were iteratively refined through rejection sampling and fine-tuned against a multi-parameter objective function encompassing predicted affinity and MHC class II binding risk. From an initial set of 50,000 sequences, this screening pipeline yielded 313 high-confidence candidates. Subsequent analysis using evolutionary scale modeling 2 (ESM2) embeddings, principal component analysis (PCA), and clustering revealed three structurally distinct clusters, with intra-cluster cosine similarities exceeding 0.99. Validation of seven representative sequences from the dominant cluster using AlphaFold3 confirmed high structural fidelity to the zolbetuximab template, demonstrating a root mean square deviation (RMSD) of 1.331 Å for the CDRH3 loop and positional deviations of less than 0.4 Å for key paratope residues. These results indicate that the designed variants preserve the core binding mode of the parent antibody. This study establishes a feasible pipeline for integrating AI-generated CDRH3 loops into functional antibody scaffolds, providing a foundation for the accelerated development of therapeutics targeting CLDN18.2 and other clinically relevant antigens.
Tao Qu, Lingyan Yuan, Weiran Cui et al.· PLoS Computational Biology· 0 citations
Accurate computational prediction of antibody-antigen binding affinity and specificity is critical for accelerating the design of next-generation therapeutics. In computational antibody design, the central challenge is not merely predicting binding, but determining whether an antibody preferentially binds its intended antigen over realistic off-targets. Existing antibody-antigen benchmarks largely focus on affinity prediction or docking accuracy on known binders, and therefore do not directly evaluate antibody specificity. We introduce SAASBench, an adversarial diagnostic benchmark that isolates antibody specificity as a set-based ranking problem. For 20 therapeutically approved full-length antibodies, SAASBench constructs an antibody-conditioned synthetic candidate set containing the true antigen and hard negative decoys drawn from the human extracellular proteome. The decoys are selected to be similar to the positive on structural plausibility of the synthetic Ab-Ag complex and on the change in solvent accessible surface area. Evaluation uses per-antibody ranking metrics aligned with practical downselection decisions. Across 20 antibody panels, affinity-based predictors display heterogeneous performance, ranging from below-random to moderate success. Overall, these results indicate that strong performance on traditional affinity benchmarks does not automatically translate into reliable antibody specificity estimation in proteome-derived settings. SAASBench provides a framework for evaluating the model's ability to estimate the specificity of a candidate antibody in relevant settings.
Dmitriy Umerenkov, Ivan Poddiakov· Proceedings of the 32nd ACM...· 0 citations
Adaptive immune receptors (AIRs), including antibodies and T-cell receptors (TCRs), mediate antigen recognition and represent a major class of therapeutic biomolecules. Their unique architecture, combining conserved framework with highly diverse complementarity-determining regions (CDRs), poses challenges for structure prediction and design. Recent advances in deep learning have transformed these fields, yet AIR-antigen interactions remain difficult targets due to limited structural data, weak co-evolutionary signals, and conformational heterogeneity. Herein, we review recent progress in structure-based deep learning approaches for AIRs, including AIR-specific language models, structure prediction, and epitope-conditioned design. We discuss commonly used datasets, evaluation metrics, and sources of bias that complicate cross-study comparisons and highlight the need for improved benchmarks. We also review emerging generative design strategies such as inverse folding, diffusion-based backbone generation, sequence-space diffusion, and sequence-structure co-design, and outline key challenges, including accurate modeling of flexible CDR loops, reliable ranking of AIR-antigen complexes, and scalable epitope-specific AIR design.
Tomer Cohen, Tanya Hochner, Dina Schneidman-Duhovny· Current Opinion in Structura...· 1 citation