Monoclonal and Polyclonal Antibodies Research

Rapidly inducible yeast surface display for antibody evolution with OrthoRep

This paper introduces an improved AHEAD platform using a synthetic β-estradiol induction system to accelerate antibody evolution in yeast.

Conditional Sequence-Structure Integration: A Novel Approach for Precision Antibody Engineering and Affinity Optimization

This paper introduces a method to design antibodies by integrating antigen structure and sequence using a protein structural encoder and antibody language model, achieving better performance than existing methods.

NanoLAS 2.0: A Comprehensive Update on a Nanobody-Focused Platform with Advanced Visualization and Docking Simulation Features

NanoLAS 2.0 updates a nanobody database with improved search, 3D visualization, docking simulation, and epitope prediction tools.

Multivalent binding model quantifies antibody species from systems serology

This paper introduces a multivalent binding model to infer antibody structural features from systems serology data, revealing insights into vaccine efficacy and disease progression.

Enhancement of antibody thermostability and affinity by computational design in the absence of antigen

This study uses DeepAb to design antibody variants with enhanced stability and affinity without antigen information, showing 91% and 94% improvements in thermal/colloidal stability and affinity, respectively.

Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors

The paper develops a computational model to analyze how bispecific antibodies interact with IL-6 and IL-8 receptors, showing how binding dynamics influence therapeutic efficacy.

Protein language models enable prediction of polyreactivity of monospecific, bispecific, and heavy-chain-only antibodies

The paper develops deep learning models using protein language models to predict polyreactivity of antibodies, outperforming structure-based models.

Mapping and Engineering Antibody-Antigen Interaction Landscapes for Systematic Affinity Enhancement

The paper introduces a method to map antibody-antigen interactions using SPID platform to enhance affinity prediction and optimize antibody design.

In silico design of stable single-domain antibodies with high affinity

This paper introduces EvolveX, a computational pipeline for designing stable single-domain antibodies with high affinity, demonstrating improved binding affinity to human targets.

For antibody sequence generative modeling, mixture models may be all you need

This paper introduces a simple generative model, SAM, for antibody sequence modeling that outperforms complex models and provides fast, interpretable tools for antibody sequence analysis.

Single-cell 5' RNA sequencing of camelid peripheral B cells reveals cellular basis of heavy-chain antibody production

The paper uses single-cell RNA sequencing to study B cell differentiation and antibody production in camels, finding that HCAb and conventional Ab B cells share similar developmental trajectories.

Simple computational methods can outperform deep learning in designing diverse, binder-enriched antibody libraries

The paper shows that simple computational methods like BLOSUM can create diverse, binder-enriched antibody libraries better than deep learning approaches.

Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders

The paper engineers ADDobody protein scaffolds to generate high-avidity ADDomer super-binders through genetic modification and structural validation.

Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling

The paper updates a tool to assess developability risks of kappa and lambda antibodies using machine learning, finding lambda antibodies have higher risk but some are more tractable.

NanoLAS: a Comprehensive Nanobody Database with Data Integration, Consolidation, and Application

NanoLAS integrates and consolidates nanobody data to provide a comprehensive database with improved search and display features, enhancing research and application potential.

VCAb: A web-tool for structure-guided antibody engineering

VCAb provides a web tool for antibody engineering by annotating antibody structures, isotypes, and mutation impacts across species.

IgDesign: In vitro validated antibody design against multiple therapeutic antigens using inverse folding

IgDesign designs antibody CDRs using deep learning and validates them in vitro, showing high success rates and improved affinities for multiple therapeutic antigens.

CD5L is a canonical component of circulatory IgM

The paper identifies CD5L as a component of circulatory IgM, showing it forms a complex with J-chain-containing pentamers and affects IgM receptor binding.

Predicting the Purity of Multispecific Antibodies From Sequence Using Machine Learning: Methods and Applications

This paper uses machine learning to predict antibody purity from sequence and format data, showing it can effectively estimate monomer percentage in multispecific antibodies.

Sample-efficient Antibody Design through Protein Language Model for Risk-aware Batch Bayesian Optimization

This paper proposes a risk-aware antibody design framework using protein language models and Bayesian optimization, showing improved efficiency and sequence quality over existing methods.

The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures

PLAbDab is a database of over 150,000 antibody sequences and structures with literature annotations, enabling searches by sequence, structure, or keyword for functional insights.

Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications

Over half of 614 commercial antibodies for 65 human neuroscience proteins failed a knockout-controlled assay, yet most targets had a well-performing antibody; recombinants performed best.

Investigations on Antarctic fish IgM drives the generation of an engineered mAb by CRISPR/Cas9

This study uses CRISPR/Cas9 to engineer a monoclonal antibody by replacing its hinge region with that of Antarctic fish IgM, resulting in a 2.5-fold higher affinity for the antigen.

Survey of commercial antibodies targeting Y chromosome-encoded genes

The paper evaluates the specificity of commercial antibodies targeting Y chromosome-encoded genes and finds many lack proper validation data.

Improving antibody affinity using laboratory data with language model guided design

The paper fine-tunes language models on laboratory data to design antibodies with improved affinity, achieving sub-25 picomolar binding for four antibodies.

Antibody Humanization via Protein Language Model and Neighbor Retrieval

This paper introduces PLAN, a machine learning model for antibody humanization, showing improved humanness scores and mutation overlap with experimental validation.

Specific attributes of the VL domain influence both the structure and structural variability of CDR-H3 through steric effects

The paper shows that VL domain attributes influence CDR-H3 structure and variability through steric effects using crystal structures and simulations.

Antibody Complementarity-Determining Region Sequence Design using AlphaFold2 and Binding Affinity Prediction Model

This paper evaluates AlphaFold2 and binder hallucination for designing high-affinity antibodies by redesigning sequences of antigen-antibody complexes.

Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire

The paper shows that genetic variation in the immunoglobulin heavy chain locus influences the diversity and characteristics of the human antibody repertoire.

Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data

The paper introduces PSERM scoring to predict antibody variant properties from deep sequencing data, showing it outperforms traditional methods in reproducibility and correlation with experimental measurements.