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Related Concept Videos

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...
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 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...
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...
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...

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A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

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Real-time ligand binding pocket database search using local surface descriptors.

Rayan Chikhi1, Lee Sael, Daisuke Kihara

  • 1Computer Science Department, Ecole Normale Supérieure de Cachan, 94235 Cachan cedex, Britanny, France.

Proteins
|May 11, 2010
PubMed
Summary
This summary is machine-generated.

Computational methods are needed to determine protein function from structure. This study presents a novel shape-based approach using Zernike moments and descriptors to predict ligand binding sites on proteins, offering competitive performance.

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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

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Last Updated: Jun 13, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

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Published on: April 3, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Structural genomics projects generate numerous protein structures with unknown functions.
  • Conventional sequence-based methods often fail to predict protein function.
  • Ligand binding prediction is crucial for understanding protein molecular function.

Purpose of the Study:

  • To develop and evaluate computational methods for characterizing protein tertiary structures.
  • To predict ligand binding sites on proteins using structural information.
  • To address the challenge of identifying protein function when sequence-based methods are insufficient.

Main Methods:

  • Developed two novel representations for ligand binding pockets based on surface properties.
  • Utilized two-dimensional pseudo-Zernike moments and three-dimensional Zernike descriptors for pocket representation.
  • Employed pocket shape comparison for ligand binding prediction against a structure database.

Main Results:

  • The proposed representations enable fast, real-time pocket searching.
  • Benchmark studies on two datasets demonstrate competitive performance against existing methods.
  • The shape-based approach effectively predicts ligand binding sites.

Conclusions:

  • The developed Zernike-based representations are effective for ligand binding site prediction.
  • Shape comparison of binding pockets is a viable strategy for protein function characterization.
  • This method offers a valuable tool for structural genomics and drug discovery.