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Related Concept Videos

Protein Networks02:26

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...
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 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...
Targets for Drug Action: Overview01:26

Targets for Drug Action: Overview

Drugs target macromolecules to modify ongoing cellular processes. Primary drug targets include receptors, ion channels, transporters, and enzymes.
Receptors are either membrane-spanning or intracellular proteins, which upon binding a ligand, get activated and transmit the signal downstream to elicit a response. Drugs bind receptors, either mimicking the action of endogenous ligands or blocking the receptor activity to bring about a modified response. Nearly 35% of approved drugs target the G...

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Related Experiment Video

Updated: May 20, 2026

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

Mapping between databases of compounds and protein targets.

Sorel Muresan1, Markus Sitzmann, Christopher Southan

  • 1DECS Global Compound Sciences, Computational Chemistry, AstraZeneca R&D, Mölndal, Sweden. sorel.muresan@astrazeneca.com

Methods in Molecular Biology (Clifton, N.J.)
|July 24, 2012
PubMed
Summary

Comparing bioactive compound and protein target databases like ChEMBL and DrugBank is crucial for drug discovery. This study analyzes four key resources, revealing content overlaps and differences to guide users in selecting optimal tools.

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Protein Target Prediction and Validation of Small Molecule Compound
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

  • Integrates cheminformatics and bioinformatics for drug discovery.
  • Focuses on the intersection of chemical structures and protein targets.

Background:

  • Databases linking bioactive compounds to protein targets are vital for drug discovery and chemical biology.
  • Assessing the utility of these resources is challenging due to diverse content and data capture strategies.

Purpose of the Study:

  • To compare the chemical and protein-level content of four major databases: ChEMBL, DrugBank, Human Metabolome Database, and Therapeutic Target Database.
  • To provide a framework for evaluating the utility of these and other similar databases in chemistry and biology research.

Main Methods:

  • Compared compound sets using NCI/CADD Structure Identifiers at varying stringencies.
  • Analyzed protein target information by mapping compounds to UniProt protein identifiers.
  • Interpreted overlaps and unique content in the context of database-specific data capture and target definitions.

Main Results:

  • Identified significant overlaps and unique chemical entities across databases, influenced by data capture strategies.
  • Observed anomalies, such as common compounds between metabolite and drug databases.
  • Found variations in protein target coverage and definitions, with ChEMBL encompassing broader chemical biology mappings.

Conclusions:

  • The comparative analysis aids users in leveraging synergies between databases like ChEMBL, DrugBank, HMDB, and TTD.
  • Provides insights for selecting appropriate databases based on specific research needs at the chemistry-biology interface.
  • Highlights the importance of understanding database-specific content and definitions for effective data utilization.