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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...
Ligand Binding and Linkage00:49

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 the...

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Related Experiment Video

Updated: Jun 17, 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

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

John A Capra1, Roman A Laskowski, Janet M Thornton

  • 1Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America.

Plos Computational Biology
|December 10, 2009
PubMed
Summary

ConCavity, a new algorithm, accurately predicts protein binding sites by combining evolutionary conservation and structural data. This tool significantly improves the identification of ligand and catalytic sites, advancing protein function research.

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Related Experiment Videos

Last Updated: Jun 17, 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
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein functional site identification is crucial for understanding molecular function.
  • Existing methods rely on structure- or sequence-based approaches.
  • There is a need for improved algorithms that integrate diverse data types.

Purpose of the Study:

  • To introduce ConCavity, a novel algorithm for predicting small molecule binding sites on protein surfaces.
  • To evaluate ConCavity's performance against existing methods for identifying ligand binding pockets and residues.
  • To explore the synergy between evolutionary sequence conservation and structure-based prediction methods.

Main Methods:

  • ConCavity integrates evolutionary sequence conservation with structure-based cavity detection.
  • Large-scale testing was performed on diverse single- and multi-chain protein structures.
  • Direct comparisons were made between conservation-based and structure-based prediction strategies.

Main Results:

  • ConCavity significantly outperforms existing methods in predicting 3D ligand binding pockets and residues.
  • The study demonstrates that conservation-based and structure-based methods offer complementary information.
  • ConCavity achieves state-of-the-art performance in predicting catalytic sites and drug binding pockets.

Conclusions:

  • ConCavity represents a significant advancement in identifying protein ligand binding sites.
  • Combining evolutionary and structural data enhances binding site prediction accuracy.
  • The findings deepen the understanding of the link between protein sequence conservation, structure, and function.