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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...
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...

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Related Experiment Video

Updated: Jun 12, 2026

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

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

Published on: April 3, 2026

3DLigandSite: predicting ligand-binding sites using similar structures.

Mark N Wass1, Lawrence A Kelley, Michael J E Sternberg

  • 1Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London, London, SW7 2AZ, UK.

Nucleic Acids Research
|June 2, 2010
PubMed
Summary
This summary is machine-generated.

3DLigandSite predicts ligand-binding sites on proteins using structural modeling. This computational tool achieves high accuracy, aiding in understanding protein function and drug discovery.

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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

Related Experiment Videos

Last Updated: Jun 12, 2026

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

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

Published on: April 3, 2026

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

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Identifying ligand-binding sites is crucial for understanding protein function and designing drugs.
  • Existing methods often require experimentally determined protein structures, which are not always available.

Purpose of the Study:

  • To develop and evaluate 3DLigandSite, a web server for predicting ligand-binding sites on protein structures.
  • To provide a computational tool that assists in structure-based drug design and protein function analysis.

Main Methods:

  • Utilizes protein structure prediction to generate models for proteins lacking experimental structures.
  • Superimposes known ligands from similar structures onto the predicted protein models to identify potential binding sites.
  • Employs the Matthew's correlation coefficient (MCC), coverage, and accuracy for performance evaluation.

Main Results:

  • Achieved an MCC of 0.64 against Critical Assessment of techniques for protein Structure Prediction (CASP8) targets.
  • Demonstrated similar performance to manual methods used in CASP8.
  • Obtained an MCC of 0.68 in further benchmarking on a large dataset of protein structures.
  • Provides visual display of predictions using an interactive Jmol applet.

Conclusions:

  • 3DLigandSite is an effective web server for predicting ligand-binding sites.
  • The tool offers valuable insights for proteins with unknown structures.
  • It serves as a useful resource for researchers in structural biology and drug discovery.