Monoclonal and Polyclonal Antibodies Research

Staged heavy-chain filtering enables Fab discovery from combinatorially intractable library spaces

This paper introduces a staged approach to Fab discovery by sequentially enriching heavy-chain variants and remating them with light-chain repertoires to overcome combinatorial complexity in antibody library screening.

SAbDab2: The structural antibody database in the age of machine learning

SAbDab2 provides updated antibody structures with machine learning-ready data and standardized splits for research.

Structural Basis of Serine Protease Inhibition by Antibodies from Biased Fab Phage-Display Libraries

The paper uses biased Fab phage-display libraries and computational methods to identify potent serine protease inhibitors and validate their binding interactions.

Monoclonal Antibody Developability from Early Assay Panels: Machine Learning for Formulation and Pharmacokinetic Risk

This paper introduces ACeT, a machine learning framework that predicts formulation and pharmacokinetic risks of monoclonal antibodies using early assay panels, achieving high predictive accuracy and interpretability.

Investigation of Intestinal Bacteria-binding Monoclonal Antibodies Derived from Rabbit Single B Cells

This study identifies and characterizes monoclonal antibodies from rabbit B cells that bind intestinal bacteria, demonstrating their broad specificity and potential for therapeutic applications.

Human lung explants as a predictive platform for evaluating the on-target, off-tumor toxicity of T cell bispecifics

This paper establishes a human lung explant model to quantify T cell bispecifics' on-target, off-tumor toxicity by measuring T cell activation and epithelial cell killing.

Specific targeting of MR1-antigen complexes using nanobodies

The paper develops a nanobody targeting MR1-5-OP-RU complexes and demonstrates its ability to modulate MAIT cell responses and act as a bispecific engager.

Development and application of nbLIBRA-seq for high-throughput discovery of antigen-specific nanobodies

This paper develops and validates nbLIBRA-seq, a method for high-throughput antigen-specific nanobody discovery in immunized alpacas, demonstrating its effectiveness in identifying nanobodies against CD71 and viral antigens.

DyAb: sequence-based antibody design and property prediction in a low-data regime

DyAb predicts antibody properties and designs new sequences with high binding affinity using a low-data approach.

A Generalization of the Ternary Binding Model to Membrane-Confined Systems with Finite Copy Number

This paper generalizes the ternary binding model to membrane-confined systems, showing geometry-dependent corrections to drug-antigen-receptor binding at nanoscale immune synapses.

A chimeric, half-life extended lysin with a unique mode of action

This paper develops a half-life extended lysin by fusing it to an Fc fragment, showing improved efficacy against staphylococcal infections through targeted release.

A Synthetic Platform for Antibody Junctional Diversification Beyond Natural Constraints

The paper introduces a synthetic platform called ARESEC that enables programmable V(D)J recombination in non-lymphoid cells, enhancing antibody junctional diversity and affinity maturation.

A functional investigation of antibody Fc-FcRn variant binding guided by *in silico* free energy perturbation methods

This paper uses free energy perturbation (FEP) calculations to predict and improve the accuracy of Fc-FcRn binding energy changes due to mutations, incorporating conformational changes and coupling effects.

AAB-seq: An antigen-specific and affinity-readable high-throughput BCR sequencing method

AAB-seq identifies antigen-binding antibodies with affinity information from single-cell BCR sequencing in immunized mice.

Self-Interaction Nanoparticle Spectroscopy Predicts High-Concentration Viscosity of Therapeutic IgG1 Antibodies

This study evaluates PS-SINS for predicting high-concentration viscosity of IgG1 antibodies, showing strong correlation with viscosity and improved model accuracy when combined with in silico data and DLS.

Mass photometry reveals stoichiometry and binding dynamics of bispecific tetravalent anti-VEGF-PD-1 antibody ivonescimab

This paper uses mass photometry to analyze the binding stoichiometry and dynamics of the bispecific antibody ivonescimab with VEGF and PD-1, finding that dimers are the most stable complex.

Predicting Antibody Self-Association with Sequence Structure Fusion Models: The Central Role of CSI-BLI in Early Developability Screening

The paper develops a sequence-structure fusion model to predict antibody self-association using CSI-BLI data, achieving high performance in distinguishing high and low self-interacting clones.

Developing Anti-EGFR/Anti-HER2 Bifunctional Antibody for Solid Tumors by Protein Engineering

This paper develops a bispecific anti-EGFR/HER2 antibody to enhance antitumor effects by targeting both receptors and improving immune responses.

Longitudinal analysis of drift in the circulating human antibody repertoire over four years

The paper analyzes changes in the human antibody repertoire over four years using high-throughput sequencing, finding conservation of broad features but changes in fine details.

ADAPT-M: A workflow for rapid, quantitative in vitro measurements of enriched protein libraries

ADAPT-M rapidly quantifies protein binder affinities and kinetics using microfluidics, enabling efficient selection of high-affinity variants from yeast-display libraries.

High-Throughput Machine Learning-Aided Antibody Discovery for Cell Surface Antigens

The paper develops a synthetic Fab yeast display library integrated with machine learning to discover antibodies against cell surface antigens, yielding hundreds of validated antibodies and a public dataset.

Structural basis for conserved and distinct antigen recognition by a lineage of malaria-protective antibodies

This study determines the structural basis of antigen recognition by two mAbs targeting PfCSP, revealing conserved and distinct binding modes and their implications for antibody function.

PANCS-spec-Binders: A system for rapidly discovering isoform- or epitope-specific binders

PANCS-spec-Binders rapidly identifies binders with defined specificity by combining selection and counterselection to target specific isoforms or epitopes.

Prediction of Antibody Non-Specificity using Protein Language Models and Biophysical Parameters

This paper predicts antibody non-specificity using protein language models and biophysical parameters, showing that heavy variable domains and isoelectric point are key predictors.

Combinatorial Optimization of Antibody Libraries via Constrained Integer Programming

This paper introduces an integer linear programming method for optimizing antibody libraries by balancing diversity and affinity, showing improved performance over baseline designs.

Multivalent Nanobodies for Potent and Broad Neutralization of Staphylococcus aureus Toxins

This paper develops multivalent nanobodies that neutralize multiple S. aureus toxins, showing potent activity in murine models of sepsis and pneumonia.

H3BERTa: A CDR-H3 specific language model for antibody repertoire analysis

H3BERTa is a transformer model trained on CDR-H3 sequences to analyze antibody repertoires, capturing immunological signatures and supporting classifier development for broadly neutralizing antibodies.

Development of an ELISA-Based Pulldown Approach for Functional Analysis of Antigen-Specific Antibodies

This paper develops an ELISA-based pulldown method to isolate functional antigen-specific antibodies from serum samples, demonstrating high specificity and sensitivity for detecting neutralising antibodies against influenza haemagglutinin.

Engineering B cells to Express Fully Customizable Antibodies with Enhanced Fc Functions

This study engineers B cells to express fully customizable antibodies with enhanced Fc functions through genome editing of the immunoglobulin Heavy chain locus.

Structural promiscuity in the human circulatory IgA1 clonal repertoire

The paper identifies structurally promiscuous IgA1 clones in human serum that exist as both monomers and J-chain-coupled dimers, challenging the view that these forms are clonally distinct.