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Related Concept Videos

Antibody Structure and Classes01:25

Antibody Structure and Classes

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.
Antibody Structure01:10

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...
Antibody Structure01:10

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...
Diversity of Antigen Receptors01:28

Diversity of Antigen Receptors

Antigen receptors are essential components of the immune system crucial in defending the body against foreign invaders. These receptors are present on the surface of B and T cells, enabling them to recognize antigens and mount an appropriate immune response.
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...
Conserved Binding Sites01:49

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 analyses the...
Antibody Actions01:26

Antibody Actions

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...

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Related Experiment Video

Updated: May 28, 2026

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
08:51

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing

Published on: March 15, 2019

Predicting antibody complementarity determining region structures without classification.

Yoonjoo Choi1, Charlotte M Deane

  • 1Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK.

Molecular Biosystems
|October 21, 2011
PubMed
Summary
This summary is machine-generated.

Antibody complementarity determining regions (CDRs) structure prediction is achieved without classification. New FREAD variants, ConFREAD and FREAD-S, improve CDR-H3 predictions and distinguish bound/unbound states.

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Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
08:09

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

Related Experiment Videos

Last Updated: May 28, 2026

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
08:51

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing

Published on: March 15, 2019

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
08:09

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

Area of Science:

  • Structural biology
  • Immunology
  • Computational biology

Background:

  • Antibodies are crucial in research, with complementarity determining regions (CDRs) mediating antigen binding.
  • Existing CDR structure classification relies on canonical structures and sequence similarity.
  • Predicting CDR structures traditionally faces challenges, especially for CDR-H3.

Purpose of the Study:

  • To predict CDR structures without prior classification.
  • To improve the accuracy of CDR-H3 structure prediction.
  • To develop methods that account for conformational changes upon antigen binding.

Main Methods:

  • Applied the FREAD loop prediction technique to CDRs.
  • Developed FREAD variants: FREAD-S (sequence similarity) and ConFREAD (contact information).
  • Tested methods on homology models and compared with RosettaAntibody; analyzed antigen-free and bound structures.

Main Results:

  • FREAD accurately predicted CDR loops (0.81-2.25 Å RMSD).
  • FREAD-S and ConFREAD significantly improved CDR-H3 prediction accuracy (1.34 Å and 1.23 Å RMSD).
  • ConFREAD successfully discriminated bound and unbound CDR structures with 1.35 Å accuracy for bound CDR-H3.

Conclusions:

  • CDR structure prediction can be treated as a general loop prediction problem, bypassing traditional classification.
  • FREAD variants offer enhanced accuracy for CDR-H3 prediction and modeling.
  • ConFREAD's ability to incorporate contact information enables discrimination of conformational states relevant to antigen binding.