Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Antibody Structure01:10

Antibody Structure

60.9K
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...
60.9K
Antibody Structure and Classes01:25

Antibody Structure and Classes

2.5K
Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
2.5K
Antibody Actions01:26

Antibody Actions

1.2K
Antibodies, or immunoglobulins, are critical players in the immune system's arsenal against invading pathogens. Produced by B cells and plasma cells, their primary role is to detect and bind to specific antigens, molecules found on the surface of pathogens like bacteria or viruses. Beyond antigen recognition, antibodies perform several vital functions that contribute to immune defense.
Neutralization
Antibodies can bind to pathogens, preventing them from infecting host cells. This process...
1.2K
Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
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...
4.3K
Protein Complex Assembly02:41

Protein Complex Assembly

10.7K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.7K

You might also read

Related Articles

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

Sort by
Same author

A planar dimer of bovine ATP synthase.

Cell death and differentiation·2026
Same author

CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV.

Frontiers in immunology·2026
Same author

Sulfur mustard exposure induces inflammatory injury by Dnmt3b-mediated DNA methylation via oleic acid accumulation in Treg cells.

Chemico-biological interactions·2026
Same author

From memorization to generalization: Why physics will improve machine learning -based prediction of protein complexes.

Current opinion in structural biology·2026
Same author

An in vivo fitness gene of Toxoplasma, MIC11, is essential for PLP1-mediated egress from host cells.

Nature communications·2026
Same author

Human DHX29 detects nonoptimal codon usage to regulate mRNA stability.

Science (New York, N.Y.)·2026

Related Experiment Video

Updated: Aug 12, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

197

AbAdapt: an adaptive approach to predicting antibody-antigen complex structures from sequence.

Ana Davila1, Zichang Xu1, Songling Li1

  • 1Research Institute for Microbial Diseases, Department of Genome Informatics, Osaka University, Suita 565-0871, Japan.

Bioinformatics Advances
|January 26, 2023
PubMed
Summary
This summary is machine-generated.

AbAdapt optimizes antibody-antigen structure modeling and docking using machine learning. This webserver accurately predicts antibody-antigen interactions, improving epitope prediction and aiding antibody design.

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

1.9K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Related Experiment Videos

Last Updated: Aug 12, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

197
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

1.9K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Immunoinformatics

Background:

  • Antibody-antigen interactions are crucial in immunology and drug development.
  • Accurate prediction of docked poses from unbound models is challenging.
  • Systematic optimization for antibody-antigen docking scoring is lacking.

Purpose of the Study:

  • To develop a webserver, AbAdapt, for modeling and docking antibody-antigen structures.
  • To optimize key steps in the modeling and docking pipeline using machine learning.
  • To improve the accuracy of epitope and paratope prediction.

Main Methods:

  • AbAdapt accepts antibody and antigen sequences as input.
  • 3D structures are modeled, followed by epitope and paratope prediction.
  • Docking is performed using Piper and Hex, with machine learning optimization.

Main Results:

  • AbAdapt achieved an 88.4% success rate in finding adequate docked poses.
  • The median rank of adequate poses was 22.
  • Epitope prediction accuracy improved, with ROC AUC increasing from 0.679 to 0.720.

Conclusions:

  • AbAdapt provides a robust platform for antibody-antigen structure prediction and docking.
  • Machine learning optimization significantly enhances prediction accuracy.
  • The tool aids in understanding antibody-antigen recognition and antibody design.