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Related Concept Videos

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...
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,...
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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

Efficiently mining protein interaction dependencies from large text corpora.

Johannes Köster1, Eli Zamir, Sven Rahmann

  • 1Genome Informatics, Institute of Human Genetics, Faculty of Medicine, University of Duisburg-Essen, Essen, Germany.

Integrative Biology : Quantitative Biosciences From Nano to Macro
|June 19, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a computational method to extract protein interaction dependencies from scientific literature. The approach efficiently identifies and visualizes these dependencies, aiding in understanding cellular networks and generating new hypotheses.

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Bioinformatics

Background:

  • Protein interactions are crucial for intracellular networks.
  • Information on these interactions is vast but unstructured in scientific literature.
  • Manual extraction of interaction dependencies is time-consuming.

Purpose of the Study:

  • To develop a computational approach for extracting protein interaction dependencies from publications.
  • To create a searchable and visualizable database of these dependencies.
  • To facilitate the understanding of cellular mechanisms and generate testable hypotheses.

Main Methods:

  • Keyword-based tokenization of full research papers.
  • Pattern matching to identify sentences describing interaction dependencies.
  • Application to the integrin adhesome network from 59,933 publications.

Main Results:

  • Extracted 208 short statements regarding interaction dependencies from the integrin adhesome network.
  • Approximately half of the extracted statements confirmed interaction dependencies.
  • Visualized a hypernetwork of protein interaction dependencies.

Conclusions:

  • The computational approach efficiently extracts valuable information on protein interaction dependencies.
  • Identified dependencies constrain feasible mechanisms in adhesion site assembly.
  • The findings generate testable hypotheses regarding the switchability of cellular processes.