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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,...
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 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...
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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Immunoprecipitation with an Anti-Epitope Tag Affinity Gel to Study Protein-Protein Interactions
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Walk-weighted subsequence kernels for protein-protein interaction extraction.

Seonho Kim1, Juntae Yoon, Jihoon Yang

  • 1Department of Computer Science, Sogang University, Seoul, Korea. shkim@lex.yonsei.ac.kr

BMC Bioinformatics
|February 27, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces novel kernel methods for extracting gene interactions from text, improving accuracy by analyzing sentence structures. The walk-weighted subsequence kernel shows promising results for biological network construction.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Natural Language Processing

Background:

  • Protein interaction networks are crucial for understanding biological processes.
  • Many protein interactions are not documented in databases and remain in raw text.
  • Automatic extraction of protein-protein interactions (PPI) from text is vital in bioinformatics.

Purpose of the Study:

  • To develop advanced kernel methods for extracting genic interactions from text.
  • To improve the analysis of structural aspects within sentences for interaction extraction.
  • To enhance the effectiveness of learning from limited training data for genic interaction extraction.

Main Methods:

  • Modification of a prior dependency kernel to include various substructures (e-walks, partial match, non-contiguous paths).
  • Proposal of a walk-weighted subsequence kernel incorporating syntactic structures, semantic roles, and lexical features.
  • Parameter weighting to differentiate the significance of syntactic locality, semantic roles, and lexical features.

Main Results:

  • The improved dependency kernel incorporates diverse substructural elements.
  • The walk-weighted subsequence kernel effectively learns structural aspects from limited data.
  • Promising results were achieved on genic interaction datasets using the walk-weighted subsequence kernel.

Conclusions:

  • The study addresses genic interaction extraction using dependency kernels and structural kernel scenarios.
  • The walk-weighted subsequence kernel demonstrated strong performance on genic interaction data.
  • Results were validated against both automatically parsed and syntactically labeled protein-protein interaction (PPI) data.