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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 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...
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...

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A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions
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A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions

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The IntAct molecular interaction database in 2010.

B Aranda1, P Achuthan, Y Alam-Faruque

  • 1EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK.

Nucleic Acids Research
|October 24, 2009
PubMed
Summary
This summary is machine-generated.

IntAct provides a comprehensive molecular interaction database with detailed annotations and a user-friendly two-tiered view for complex query development and data exploration. This open-source resource facilitates access to curated binary interaction evidence.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Molecular Biology

Background:

  • The IntAct database serves as a crucial resource for molecular interaction data.
  • Expert curators meticulously extract and annotate data from scientific literature and direct submissions.
  • A deep annotation model ensures a high level of detail in the stored information.

Purpose of the Study:

  • To present the IntAct database and its toolkit for managing and accessing molecular interaction data.
  • To introduce a new two-tiered data view addressing growing data volume and user needs.
  • To enhance user experience through advanced querying and data visualization capabilities.

Main Methods:

  • Data abstraction from literature and direct depositions by expert curators.
  • Implementation of a deep annotation model with hierarchical controlled vocabularies.
  • Development of a two-tiered data view with an iterative complex query interface and specialized views.

Main Results:

  • As of September 2009, IntAct contained over 200,000 curated binary interaction evidences.
  • A new search interface enables iterative development of complex queries.
  • Results are presented in a simplified tabular view, with specialized views for detailed exploration.

Conclusions:

  • IntAct offers a robust, open-source platform for molecular interaction data.
  • The enhanced two-tiered view improves data accessibility and query complexity.
  • The database and its source code are freely available for research and development.