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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...
Drug Discovery: Overview01:26

Drug Discovery: Overview

Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
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...
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 Videos

BindingDB and ChEMBL: online compound databases for drug discovery.

Anne Mai Wassermann1, Jürgen Bajorath

  • 1Department of Life Science Informatics , B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D 53113 Bonn , Germany +49 228 2699 306 ; +49 228 2699 341 ; bajorath@bit.uni-bonn.de.

Expert Opinion on Drug Discovery
|June 2, 2012
PubMed
Summary
This summary is machine-generated.

Public domain databases like BindingDB and ChEMBL are crucial for pharmaceutical research, offering vital compound structure and activity data. These resources support drug discovery, chemoinformatics, and collaborations between academia and industry.

Related Experiment Videos

Area of Science:

  • Drug discovery and development
  • Chemoinformatics
  • Bioinformatics

Background:

  • Public domain repositories are essential for pharmaceutical research, particularly in academic settings.
  • Databases provide critical structure-activity data for mining and evaluating drug design methods.
  • These resources facilitate scientific collaboration between academic and commercial entities.

Purpose of the Study:

  • To highlight two major public domain compound data repositories: BindingDB and ChEMBL.
  • To discuss their different origins and development environments.
  • To emphasize their complementary roles in providing compound activity information.

Main Methods:

  • Review of public domain compound data repositories.
  • Comparison of BindingDB (academic origin) and ChEMBL (biotechnology origin).
  • Integration of data with PubChem bioassays for comprehensive analysis.

Main Results:

  • BindingDB and ChEMBL offer substantial, complementary compound activity data.
  • Both databases primarily source information from the scientific literature.
  • They cover various stages of compound exploration and optimization.

Conclusions:

  • BindingDB and ChEMBL are foundational resources for public domain compound data analysis.
  • These repositories are indispensable for structure-activity relationship studies and chemoinformatics.
  • Their continued development supports advancements in pharmaceutical research.