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Related Concept Videos

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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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:
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Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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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...
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Protein-protein Interfaces

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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...
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Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Conserved Binding Sites

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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.
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BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data.

Tiqing Liu1, Linda Hwang1, Stephen K Burley2

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Summary

BindingDB, a public database of protein-small molecule binding affinities, now features 2.9 million measurements. This expansion, driven by patent data curation, enhances its utility for drug discovery and AI model development.

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Area of Science:

  • Biochemistry
  • Medicinal Chemistry
  • Computational Biology

Background:

  • BindingDB is a public database for experimentally measured binding affinities.
  • It supports applications in medicinal chemistry, pathway annotation, and AI model training.
  • Previous updates were published in 2016.

Purpose of the Study:

  • To report significant growth and enhancements in the BindingDB database since 2016.
  • To highlight new features and data acquisition strategies.
  • To discuss BindingDB's role and future development.

Main Methods:

  • Curation of binding affinity data from US patents.
  • Website redesign using responsive web design principles.
  • Implementation of enhanced search, filtering, and data download options.

Main Results:

  • Database now contains 2.9 million binding measurements for 1.3 million compounds and thousands of protein targets.
  • Substantial influx of novel binding data from patent curation.
  • Improved website usability, data accessibility, and long-term data archiving.

Conclusions:

  • BindingDB has experienced significant growth and improvement.
  • Enhanced data accessibility and new features support diverse scientific applications.
  • Continued development and open data policies position BindingDB as a key resource.