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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...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Published on: March 3, 2015

Extracting interactions between proteins from the literature.

Deyu Zhou1, Yulan He

  • 1Informatics Research Centre, The University of Reading, Reading, RG6 6BX, UK. d.zhou@reading.ac.uk

Journal of Biomedical Informatics
|January 22, 2008
PubMed
Summary
This summary is machine-generated.

Biomedical research generates vast data and publications. This review outlines text mining methods for extracting knowledge, focusing on protein-protein interactions discovery from biomedical texts.

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Area of Science:

  • Biomedical Informatics
  • Computational Biology
  • Text Mining

Background:

  • Biomedicine has seen rapid advancement, generating extensive experimental and computational data.
  • An exponential rise in publications necessitates efficient knowledge discovery tools.
  • Text mining is crucial for extracting specific biological insights, like protein-protein interactions.

Purpose of the Study:

  • To outline information extraction methods in the biomedical domain.
  • To focus on the discovery of protein-protein interactions using text mining.
  • To categorize and exemplify current biomedical information extraction techniques.

Main Methods:

  • Surveying methodologies for analyzing and processing plain biomedical texts.
  • Categorizing existing work in biomedical information extraction.
  • Presenting examples of applied information extraction methods.

Main Results:

  • Identified various information extraction techniques applicable to biomedical literature.
  • Categorized approaches for discovering protein-protein interactions.
  • Provided illustrative examples of these methods in practice.

Conclusions:

  • Text mining offers valuable tools for navigating the growing biomedical literature.
  • Effective extraction of protein-protein interactions is key for advancing biological research.
  • Challenges in the field were discussed, with potential solutions proposed.