Monoclonal and Polyclonal Antibodies Research

50 years of antibody numbering schemes: a statistical and structural evaluation reveals key differences and limitations

The paper evaluates antibody numbering schemes using statistical and structural analyses, identifying discrepancies in CDR definitions and highlighting the need for refinement.

Humatch - fast, gene-specific joint humanisation of antibody heavy and light chains

Humatch provides fast, gene-specific humanisation of antibody heavy and light chains using CNNs, aligning with experimental data and reducing immunogenic risks.

De novo non-compartmentalized microorganism for directed evolution of nanobodies

This study designs a de novo microorganism, Syn-phage, to evolve nanobodies with improved properties for super-resolution live-cell imaging of endogenous proteins.

A computationally guided approach to improve expression of VHH binders

This paper improves VHH binder expression through computational modeling of hydrophobic hotspots and guided mutagenesis.

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

RIOT annotates immunoglobulin sequences by handling nucleotide and amino acid data, using an open germline database, and improving speed and accuracy over existing tools.

A biosensor-based phage display selection method for automated, high-throughput Nanobody discovery

This paper introduces a biosensor-based phage display method for high-throughput Nanobody discovery, reducing time and labor by using automated Octet biolayer interferometry.

Novel Library Assembly Technique for Developing Nanobodies Targeting IPNv VP2 Protein

This paper develops a novel nanobody library assembly technique for targeting IPNv VP2 protein, identifying specific nanobodies with diagnostic potential.

p-IgGen: A Paired Antibody Generative Language Model

p-IgGen generates paired heavy-light chain antibodies with biophysical properties similar to clinical-stage therapeutics.

Learning antibody sequence constraints from allelic inclusion

The paper uses allelic inclusion data to train models that identify antibody sequence constraints, finding stronger correlations with antibody properties than existing methods.

Addressing the antibody germline bias and its effect on language models for improved antibody design

This study addresses germline bias in antibody language models by developing AbLang-2, which predicts non-germline residues more effectively than existing models.

CXADR is a Human IgG Fc Receptor

The paper identifies CXADR as a human IgG Fc receptor, demonstrating its non-paratope-specific binding to human and rabbit IgG and its role in linking the humoral immune system to previously unknown cell types.

An adaptive autoregressive diffusion approach to design active humanized antibody and nanobody

This paper introduces HuDiff, a diffusion model for humanizing antibodies and nanobodies, showing improved similarity to experimentally humanized sequences and enhanced binding affinity.

Making the effect visible - OX40 targeting nanobodies for in vivo imaging of activated T cells

This paper develops nanobodies targeting hOX40 for in vivo imaging of activated T cells, showing they bind specifically and function as imaging probes without affecting T cell viability.

Elucidating key determinants of engineered scFv antibody in MMP-9 binding using high throughput screening and machine learning

The paper uses high-throughput screening and machine learning to identify key determinants of scFv antibody binding to MMP-9.

Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms

Seq2scFv annotates and characterizes scFv sequences from long-read sequencing data to improve antibody discovery.

Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs

The paper benchmarks generative models for antibody sequence design using log-likelihood scores and finds they correlate with binding affinities, suggesting their potential for ranking.

Computational design of developable therapeutic antibodies: efficient traversal of binder landscapes and rescue of escape mutations

This paper presents a computational pipeline for designing therapeutic antibodies using AI and physics-based methods, showing improved binding and developability across SARS-CoV-2 variants.

PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature

PLAbDab-nano is a database of 5000 annotated VHH and VNAR nanobody sequences from camelids and sharks, providing a resource for designing libraries and finding similar sequences.

IgBlend: Unifying 3D Structures and Sequences in Antibody Language Models

IgBlend integrates 3D structures and sequences for antibody language models, outperforming existing models in benchmarks and showing correlation with binding affinities.

Development of nanobodies against human Survivin, applicable to suppress cell proliferation.

This study develops nanobodies against human Survivin that suppress cell proliferation by disrupting cell cycle regulation.

IgGM: A Generative Model for Functional Antibody and Nanobody Design

IgGM is a generative model that designs functional antibodies and nanobodies by predicting sequences and structures simultaneously for a given antigen.

Improvement of Antibody Affinity and Using PURE Ribosome Display and Microbial Secretion System

The paper develops a method combining PURE ribosome display, NGS, and microbial secretion to identify high-affinity antibody variants.

Guiding diffusion models for antibody sequence and structure co-design with developability properties

This paper designs antibody sequences and structures using a diffusion model guided by developability properties like solubility and folding stability.

Targeted protein degradation in lysosome utilizing naturally produced bifunctional antibodies with high levels of mannose 6-phosphate glycans

This paper develops a method to produce bifunctional antibodies with high mannose 6-phosphate glycans for lysosomal degradation of target proteins.

Evaluation of High-Affinity Monoclonal Antibodies and Antibody-Drug Conjugates by Homogenous Time-Resolved FRET

This paper develops a competition assay using homogenous TR-FRET to rank the affinities of high-affinity monoclonal antibodies and antibody-drug conjugates for a common antigen, enabling scalable and low-cost evaluation.

Function-first discovery of high affinity monoclonal antibodies using Nanovial-based plasma B cell screening

This paper introduces Nanovials for function-first antibody discovery, enabling high-affinity antibody identification against membrane-bound targets.

Comprehensive assembly of monoclonal and mixed antibody sequences

This paper introduces Fusion, a de novo assembler for antibody sequences, demonstrating high accuracy in reconstructing monoclonal and mixed antibody sequences from mass spectrometry data.

Recombinant and synthetic affibodies function comparably for modulating protein release

This study compares synthetic and recombinant BMP-2-specific affibodies, finding they have similar structure and function but synthetic ones have lower endotoxin levels and higher yield.

Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability

The paper quantifies the plasticity of antibody developability by analyzing sequence and structure-based parameters in natural and human-engineered antibodies.

Development of a humanized anti-FABP4 monoclonal antibody for treatment of breast cancer

This paper develops humanized anti-FABP4 monoclonal antibodies that inhibit breast cancer tumor growth and metastasis by targeting FABP4's role in lipid metabolism.