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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...
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...
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 23, 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

BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures.

Zeyar Aung1, Joo Chuan Tong

  • 1Institute for Infocomm Research, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore. azeyar@i2r.a-star.edu.sg

Genome Informatics. International Conference on Genome Informatics
|May 9, 2009
PubMed
Summary
This summary is machine-generated.

We developed BSAlign, a new graph-based method for identifying protein ligand-binding sites. BSAlign is 14x faster than existing methods, aiding rapid drug discovery by efficiently finding similar binding sites.

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Last Updated: Jun 23, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions
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An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions

Published on: March 14, 2016

Area of Science:

  • Structural Bioinformatics
  • Computational Drug Discovery

Background:

  • Identifying ligand-binding sites in proteins is vital for drug discovery.
  • Existing methods can be time-consuming for large-scale protein analysis.

Purpose of the Study:

  • To introduce BSAlign, a novel and rapid method for detecting protein binding sites similar to a known query site.
  • To improve the efficiency of binding site detection for applications like drug discovery.

Main Methods:

  • Representing protein structures and binding sites as graphs.
  • Utilizing a subgraph isomorphism algorithm for efficient similarity detection.
  • Comparing BSAlign's performance against the established SiteEngine method.

Main Results:

  • BSAlign demonstrates a 14-fold increase in speed compared to SiteEngine.
  • Both BSAlign and SiteEngine achieve 60% accuracy in identifying adenine-binding sites.
  • The method maintains accuracy while significantly reducing processing time.

Conclusions:

  • BSAlign offers a highly efficient solution for detecting similar ligand-binding sites.
  • The speed of BSAlign makes it suitable for speed-critical applications such as large-scale drug discovery.
  • The BSAlign program is publicly available for use and further development.