Monoclonal and Polyclonal Antibodies Research

The Quagmire of Immunogenicity-Guided Antibody Design: Labels Limit Progress

The paper evaluates antibody design methods using immunogenicity labels and finds that format-based approaches outperform sequence-based predictors, but label inaccuracies limit progress.

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.

Multi-resolution humanness scoring of antibodies via a region-isolated language model

The paper introduces IgScope, a language model for antibody humanness scoring at multiple resolutions, showing improved accuracy over existing methods and revealing issues with generative models.

Affinity Maturation Enables Dual Targeting of Cancer-Associated MUC1-Tn/STn and Drives Potent Tumor Control

This study affinity-matures an antibody to recognize both MUC1-Tn and MUC1-STn glycoforms, enhancing its efficacy against heterogeneous tumors.

Design of full-length agonist and antagonist antibodies for hard targets

This paper designs full-length agonist and antagonist antibodies for hard targets using a computational pipeline, achieving nanomolar affinities and functional activity.

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.

Sequence-only antigen context improves modeling of antibody hypervariable regions

This paper introduces LangAAI, a sequence-only model that improves antibody CDR design by conditioning on antigen sequences, showing better performance than existing methods without requiring 3D structures.

High-throughput affinity profiling of antibodies against soluble and native membrane targets by digital flow cytometry

This paper introduces digital flow cytometry assays for high-throughput, quantitative affinity measurements of antibodies against both soluble and membrane targets.

Domain-resolved epitope mapping of B7-H3-targeting VHH-Fcs defines isoform-selective binders for antibody-drug conjugate development

The paper maps epitopes of B7-H3-targeting VHH-Fcs to identify isoform-selective binders for antibody-drug conjugate development.

What comes after de novo? Automated lead optimization of proteins with CRADLE-1

CRADLE-1 automates protein lead optimization, improving speed and efficiency compared to rational design methods.

Affinity maturation of a single-domain antibody via rational mutagenesis informed by artificial intelligence

The paper uses AI-predicted protein structures to guide rational mutagenesis of a single-domain antibody, enhancing its binding affinity to IL-12 by eightfold.

RNA evidence supports clinical stage antibody drug targets in oncology

The paper evaluates whether single-cell RNA-seq improves the prioritization of antibody-based oncology targets by combining tumor specificity, normal safety, and blood sink features.

BCR repertoire analysis and cloning of antibody candidates targeting native and Asp7-isomerized β-amyloid

The paper demonstrates a repertoire-guided workflow to prioritize antibody candidates targeting β-amyloid and its isoAsp7 proteoform, identifying potential heavy-light chain combinations through computational and experimental methods.

kitAb: an automated framework for assay-specific antibody developability modeling and large-scale landscape analysis

kitAb provides an automated framework for antibody developability modeling and landscape analysis, showing comparable performance to existing methods while being faster.

Differential Effects of Distinct Type I Interferons and IFN Inducers on Fc Receptor landscape and myeloid cell function

This study examines how different type I interferons and IFN inducers affect Fc receptor expression and function in myeloid cells, revealing cell-type- and stimulus-specific modulation patterns.

C1q-mediated steric hindrance limits FcγR contribution to antibody-driven phagocytosis by human neutrophils

This study shows that complement proteins like C1q block FcγR engagement with IgG, reducing their role in neutrophil phagocytosis, while complement receptors still enhance bacterial clearance.

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.

IgG4 antibody repertoire diversity is stable over several years in health and autoimmune disease

The paper examines IgG4 antibody repertoire stability over time in health and autoimmune diseases, finding that most clones remain stable despite treatment.

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.

Inhibitory Fc Receptor sets a time limit on macrophage response to IgG

The paper shows that inhibitory Fc{gamma}RIIB limits macrophage signaling duration, while activating Fc receptors control sensitivity, using chimeric receptors and in silico modeling.

MIMOSA: Guiding De Novo Antibody Design with Natural Interaction Fingerprints

MIMOSA improves de novo antibody design by constraining generative models to known binder interfaces, achieving validated binders on targets where unconstrained methods fail.

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.

Size-dependent effect of site-specific polyethylene glycol modification of trastuzumab on the antibody functions

This study evaluates how site-specific PEG modification and PEG size affect trastuzumab's antibody functions, finding size-dependent reductions in ADCC activity and antigen/Fc receptor interactions.

An interpretable open platform for sequence-based antibody developability prediction

DELPHI is an open platform for predicting antibody developability from sequence, achieving high AUC scores and enabling residue-level engineering insights.

Optimization of a Human Anti-polio Monoclonal Antibody as a Potential Therapeutic Modality

This paper optimizes a human monoclonal antibody against poliovirus to improve its serum half-life and manufacturability through sequence engineering and experimental evaluation.

nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis

nanorepertoire is an end-to-end Nextflow pipeline for analyzing camelid nanobody repertoires, providing standardized and reproducible analysis of AIRR-seq data.

A bispecific antibody targeting a membrane-proximal ASGPR1 region promotes TNF-α recruitment and uptake

This paper develops a bispecific antibody that redirects TNF-α into cells by binding ASGPR1, showing reduced TNF release from HepG2 cells.

SixPack-AbScan: a web server to discover cross-reactivity of antibodies across species

SixPack-AbScan is a web server that computationally screens antibodies for cross-reactivity across species using epitope conservation.

A Turing-Style Test for In-Silico Antibodies: How Sampling Mode Makes WGAN-GP Beat VAE in the Wet Lab

This paper compares GANs and VAEs for generating viable antibody sequences, finding GANs outperform VAEs when sampling strategies are optimized.