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Related Concept Videos

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...
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...
Ligand Binding Sites02:40

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 Sites02:40

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...
Protein-protein Interfaces02:04

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...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 20, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Protein-binding site prediction based on three-dimensional protein modeling.

Mina Oh1, Keehyoung Joo, Jooyoung Lee

  • 1School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea.

Proteins
|September 22, 2009
PubMed
Summary

This study presents a two-stage method for predicting protein ligand binding sites using structural templates. The approach achieves high accuracy, even when ligand identity is unknown, aiding protein function studies.

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Last Updated: Jun 20, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Protein structure dictates function, with ligand binding being a key biochemical activity.
  • Accurate prediction of ligand binding sites is crucial for understanding protein function and drug discovery.

Purpose of the Study:

  • To develop and evaluate a two-stage template-based method for predicting protein ligand binding sites.
  • To assess the method's performance on CASP8 targets, comparing predictions to native structures.

Main Methods:

  • A two-stage approach utilizing template structures for both protein modeling and binding site prediction.
  • Structural clustering of ligand-containing templates applied to predicted protein models.
  • Prediction performed irrespective of known ligand identities.

Main Results:

  • High-quality results achieved on CASP8 targets with accuracy/coverage of 70%/80%.
  • Performance closely matched predictions from native protein structures.
  • Successful predictions were obtained even when using different ligand molecules than the actual bound ligands.

Conclusions:

  • The template-based method is effective for predicting protein ligand binding sites.
  • The approach demonstrates robustness, performing well even without prior knowledge of specific ligands.
  • This method can be integrated with experimental techniques for systematic investigation of protein activities.