Monoclonal and Polyclonal Antibodies Research

This study identifies two IgY subclasses in snakes through structural and phylogenetic analysis, revealing divergent disulfide bond architectures and functional constraints.

This study benchmarks compact transformer models for de novo antibody design, finding no significant architectural differences in performance at small scales.

This study shows Fc-silencing mutations in therapeutic antibodies do not block FCRL5 binding, potentially affecting B cell function through novel Fc-FCRL5 interactions.

The paper generates and validates synthetic epitope proteins to improve de novo antibody design by combining computational design with high-throughput experimental binding data.

The paper presents a computational workflow for designing nanobody binders against a novel cancer target, achieving sub-nanomolar affinities without experimental structure or prior antibody data.

KyDab is a database of antibody discovery selection campaigns that provides full-funnel selection data for AI model development and evaluation.

This study develops mRNA-based Fc-free scFv antibodies targeting Pseudomonas aeruginosa's type III secretion system, showing efficacy in treating multidrug-resistant airway infections in mice.

This paper introduces a model that separates mutation and selection processes in antibody language models to improve prediction of mutation effects on antibody function.

This paper introduces AbNatiV2 and p-AbNatiV2, deep learning models for assessing nativeness and pairing likelihood in antibodies and nanobodies, showing improved performance on held-out tests.

This study combines a homogenous KIM-1-targeted ADC with sunitinib to treat RCC, showing synergistic antitumor efficacy in a mouse model.

The paper evaluates how different linker designs affect the structure and function of an anti-GUCY2C scFv using computational methods.

This paper reports four novel VHHs against VEEV E2 protein selected using computational and biochemical strategies, showing they can bind and sequester viral particles, acting as viral sponges.

This paper develops monoclonal antibodies specific for citrullination, showing high sensitivity and minimal cross-reactivity with homocitrullination.

The paper disentangles protein-interaction and protein-quality effects in antibody-antigen binding using deep mutational scanning and evaluates models for their ability to predict these effects.

This study uses molecular dynamics simulations to predict antibody internalization by mapping energy landscapes between antibodies and JAM-A receptors, identifying key interactions that drive endocytosis.

SpeciefAI generates species-specific mRNA and protein sequences for antibodies and nanobodies using a transformer model trained on six species.

This paper introduces IASO, a sequence-centric framework for designing therapeutic scFvs and multi-specific engagers using only antigen sequence, demonstrating its ability to identify novel binders and overcome drug resistance.

This paper elucidates the mechanistic basis for the selective recognition of FcγRIIa by monoclonal antibody IV.3 through a combination of experimental and computational methods.

The paper develops NanoMAP, a pipeline for analyzing nanobody repertoires, showing it outperforms standard methods in identifying coherent clonal families and detecting high-affinity nanobodies.

The paper generates antigen-specific recombinant bat antibodies from Pteropus alecto to study bat antibody immunity and provides new diagnostic tools.

The paper evaluates the developability of single-domain antibody chelator conjugates for diagnostic radiotracers using stability and functional assays.

This paper presents a methyl group assignment for the Fc fragment of an IgG1 antibody using NMR, enabling structural analysis of glycosylated Fc without isotopic labelling.

The paper introduces CaptureBody, a bispecific antibody for spectral flow cytometry that improves unmixing accuracy by using cells instead of compensation particles.

This study compares mRNA and yeast display technologies for evaluating ML-designed miniprotein binders, finding mRNA display better enriches slow dissociating binders and achieves higher library coverage.

The paper develops the ASD database to aggregate antibody-antigen interaction data from multiple sources, providing a standardized resource for computational model development.

This study demonstrates that non-targeted immunization and panning can isolate PSMA-targeting nanobodies from phage display libraries.

This study identifies multiple IgM gene variants in geckos and analyzes their evolutionary origin and functional divergence through sequence and structural comparisons.

This study evaluates the cytotoxic mechanism of IMV-M, a MUC16 x DR5 bispecific antibody, showing that multivalent MUC16 binding is required for cytotoxicity and that CA125 does not neutralize its activity.

Ophiuchus-Ab is a generative foundation model for antibody design that captures inter-chain dependencies and predicts antibody properties like developability and binding affinity.

alpseq is an open-source pipeline for processing NGS data from nanobody libraries, enabling efficient analysis and identification of enriched sequences.