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

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

You might also read

Related Articles

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

Sort by

Same author

Nanoscale Optical Inhomogeneities From Compositional Segregation Within Individual GaN-on-Si Quantum Wells.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same author

The Role of Defect Geometry in Localized Emission from Monolayer Tungsten Dichalcogenides.

ACS nano·2026

Same author

scDeepAPA: a deep learning framework for single-cell alternative polyadenylation identification.

Briefings in bioinformatics·2026

Same author

Strong effect of the nonpolar solvent molecular structure on CdSe nanoplatelet stacking.

Nanoscale·2026

Same author

VIRSE: a variational Bayesian framework for RNA structural ensemble inference.

Briefings in bioinformatics·2026

Same author

Socioeconomic and Clinical Determinants Driving Access to BRCA Genetic Testing in Cancer : A Case-Control Study Using Observational Electronic Health Records Across Multiple Sites.

medRxiv : the preprint server for health sciences·2026

Search research articles

Related Experiment Video

Updated: Jun 16, 2025

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

AntiFormer: graph enhanced large language model for binding affinity prediction.

Qing Wang¹, Yuzhou Feng^2,3, Yanfei Wang¹

¹Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, FL 32611, USA.

Briefings in Bioinformatics

|August 20, 2024

Summary

This summary is machine-generated.

AntiFormer, a new AI tool, accurately predicts antibody binding affinity, accelerating the development of antibody-based therapeutics and diagnostics. It identifies potent antibodies against SARS-CoV-2 and reveals age-related differences in immune responses to influenza vaccines.

Keywords:

antibody binding affinity antibody maturation large language model single-cell BCR

More Related Videos

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

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Related Experiment Videos

Last Updated: Jun 16, 2025

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

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

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Area of Science:

Immunology
Computational Biology
Bioinformatics

Background:

Antibodies are crucial for immune defense and therapeutics.
Assessing antibody-antigen binding affinity is vital but challenging with current methods.
Affinity maturation refines antibody specificity and binding strength through somatic mutations.

Purpose of the Study:

To introduce AntiFormer, a graph-based large language model for predicting antibody binding affinity.
To evaluate AntiFormer's performance against existing methods for antibody affinity prediction.
To apply AntiFormer to identify neutralizing antibodies and understand immune response variations.

Main Methods:

Developed AntiFormer, a graph-based large language model integrating antibody sequence information.
Evaluated AntiFormer's predictive accuracy and computational efficiency.
Applied AntiFormer to analyze antibody responses in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients and influenza vaccine recipients.

Main Results:

AntiFormer demonstrated superior performance in predicting antibody binding affinity compared to existing methods.
The model achieved accurate predictions with reduced computational time.
Identified potent neutralizing antibodies against SARS-CoV-2 and elucidated age-related differences in antibody responses to influenza vaccination, particularly in young individuals.

Conclusions:

AntiFormer offers a powerful computational approach to accelerate antibody discovery and development.
The findings highlight the importance of large clonotype categories in affinity maturation and immune modulation.
AntiFormer provides valuable insights for therapeutic strategies, vaccine development, and understanding immune response dynamics.