Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Affinity and Avidity

Affinity and Avidity

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Antibody Structure

Antibody Structure

Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Electrokinetic Chromatography-based Micro Methods for Separation and Physiochemical Characterization of Very Hydrophobic Pharmaceuticals.

Journal of separation science·2025

Same author

Quantitation of native and forced degraded collagens by capillary zone electrophoresis: Method development and validation.

Journal of separation science·2023

Same author

Design of experiments for micellar electrokinetic chromatography method development for the monitoring of water-soluble vitamins in cell culture medium.

Electrophoresis·2023

Same author

Strategies for capillary electrophoresis: Method development and validation for pharmaceutical and biological applications-Updated and completely revised edition.

Electrophoresis·2023

Same author

Experimentally Observed Conformational Changes in Antibodies Due to Binding and Paratope-epitope Asymmetries.

Journal of pharmaceutical sciences·2023

Same author

An interlaboratory capillary zone electrophoresis-UV study of various monoclonal antibodies, instruments, and ε-aminocaproic acid lots.

Electrophoresis·2023

Search research articles

Related Experiment Video

Updated: Mar 19, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

AbDist: a lightweight, distance-based model for antibody affinity prediction as an interpretable benchmark for

Marc Hoffstedt¹, Jannis Wowra¹, Hermann Wätzig¹

¹Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany.

|March 18, 2026

Summary

A new distance-based model, AbDist, predicts antibody affinity using local sequence environments. It matches complex models in performance while being faster, more interpretable, and suitable for early-stage antibody engineering.

Keywords:

Antibody Affinity Benchmarking Distance-Based Machine Learning

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Published on: February 8, 2021

Related Experiment Videos

Last Updated: Mar 19, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Rapid Determination of Antibody-Antigen Affinity by Mass Photometry

Published on: February 8, 2021

Area of Science:

Biochemistry
Computational Biology
Immunology

Background:

Complex models for antibody affinity prediction exist.
Simple distance-based models show promise in related fields like T-cell receptor epitope prediction.
These simpler models offer advantages in interpretability and computational efficiency.

Purpose of the Study:

To develop a novel distance-based model for antibody affinity prediction.
To assess the effectiveness of local sequence environments for featurization.
To provide an interpretable and efficient tool for antibody engineering.

Main Methods:

Developed AbDist, a distance-based computational model.
Utilized fragments around mutation sites for sequence featurization.
Applied AbDist to classification and regression tasks on public datasets.

Main Results:

AbDist performance matches state-of-the-art machine learning models.
The model demonstrates that local sequence environments are sufficient for effective featurization.
AbDist is computationally efficient and interpretable.

Conclusions:

AbDist is a viable, efficient, and interpretable alternative for antibody affinity prediction.
The model is well-suited for data-sparse, early-stage antibody engineering.
It shares limitations in out-of-distribution generalization with current models.