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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...

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...

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 analyses the...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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:

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Related Experiment Video

Updated: May 11, 2026

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

EpiDOCK: a molecular docking-based tool for MHC class II binding prediction.

Mariyana Atanasova¹, Atanas Patronov, Ivan Dimitrov

¹School of Pharmacy, Medical University of Sofia, 2 Dunav street, 1000 Sofia, Bulgaria.

Protein Engineering, Design & Selection : PEDS

|May 11, 2013

Summary

EpiDOCK is a new tool that predicts which peptides bind to human leukocyte antigen (HLA) proteins, crucial for cellular peptide vaccines. This structure-based server accurately identifies potential T-cell epitopes, aiding vaccine development.

Keywords:

MHC class II binding prediction docking peptide vaccines quantitative matrices

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Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

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Last Updated: May 11, 2026

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

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Published on: March 25, 2014

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

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Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Published on: October 15, 2021

Area of Science:

Immunoinformatics
Structural Biology
Vaccine Development

Background:

Cellular peptide vaccines rely on T-cell epitopes, which must bind to major histocompatibility complex (MHC) proteins.
Identifying peptide-MHC binders is experimentally challenging due to the high polymorphism and polygenicity of human MHCs, known as human leukocyte antigen (HLA).

Purpose of the Study:

To introduce EpiDOCK, the first structure-based computational server for predicting peptide binding to MHC class II molecules.
To provide a tool for accurate identification of T-cell epitopes for vaccine design.

Main Methods:

Developed EpiDOCK, a novel structure-based server for MHC class II binding prediction.
The server focuses on predicting binding to the 23 most frequent human MHC class II proteins.

Main Results:

EpiDOCK achieves 90% accuracy in identifying true binders and 76% in identifying true non-binders.
The overall prediction accuracy of EpiDOCK is 83% for MHC class II peptide binding.
The server is freely accessible online for research purposes.

Conclusions:

EpiDOCK offers a significant advancement in predicting peptide-MHC class II binding.
This tool can accelerate the identification of T-cell epitopes, facilitating the development of effective cellular peptide vaccines.