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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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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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Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Receptor databases and computational websites for ligand binding.

Brinda K Rana1, Philip E Bourne, Paul A Insel

  • 1Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA. bkrana@ucsd.edu

Methods in Molecular Biology (Clifton, N.J.)
|June 8, 2012
PubMed
Summary
This summary is machine-generated.

This chapter provides a curated list of websites and computational tools for studying receptor-ligand interactions. These resources aid researchers in understanding cellular regulation, drug interactions, and receptor function.

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Area of Science:

  • Biochemistry
  • Pharmacology
  • Bioinformatics

Background:

  • Receptor-ligand interactions are crucial for cellular processes regulated by neurotransmitters, hormones, and drugs.
  • Receptor genes constitute the largest functional gene families in mammalian genomes, driving extensive research.
  • Computational tools have been developed to predict receptor-ligand interactions in silico.

Purpose of the Study:

  • To provide a comprehensive list of public domain websites and computational tools for receptor-ligand interaction studies.
  • To facilitate both experimental and computational research in the field of receptor binding.
  • To support the utilization of large datasets for modeling, drug pattern analysis, and receptor comparisons.

Main Methods:

  • Compilation of publicly available websites and Uniform Resource Locators (URLs).
  • Inclusion of databases for receptor sequences (e.g., G-protein-coupled receptors, nuclear receptors) and binding assay results.
  • Integration of computational tools for interaction modeling and orphan receptor function prediction.

Main Results:

  • A curated list of websites offering data and tools for receptor-ligand binding studies is presented.
  • Resources include sequence databases, experimental binding data, and predictive computational tools.
  • The provided list facilitates diverse research applications, from structure-function modeling to drug discovery.

Conclusions:

  • The curated websites serve as a valuable resource for researchers investigating receptor-ligand interactions.
  • These online tools and databases support experimentalists and computational scientists alike.
  • The resource aims to advance the understanding of cellular signaling and drug development through accessible data and tools.