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

Published on: March 3, 2015

Protopia: a protein-protein interaction tool.

Alejandro Real-Chicharro1, Iván Ruiz-Mostazo, Ismael Navas-Delgado

  • 1University of Malaga and CIBER de Enfermedades Raras, Department of Molecular Biology and Biochemistry, Faculty of Sciences, Instituto de Salud Carlos III, Spain. areal@lcc.uma.es

BMC Bioinformatics
|October 16, 2009
PubMed
Summary
This summary is machine-generated.

Protopia is a new biological tool that searches and integrates protein interaction data from multiple databases. It helps detect redundancies and visualize complex protein networks for better analysis.

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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

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interactions are fundamental to cellular organization and homeostasis.
  • Increasing experimental data necessitates computational tools for integration and organization.
  • Existing biological databases contain vast amounts of protein interaction information.

Purpose of the Study:

  • To present Protopia, a novel biological tool for searching and integrating protein interaction data.
  • To facilitate the organization and analysis of biological data through a multidisciplinary initiative.
  • To provide a unified platform for accessing diverse Protein Interaction Web Databases.

Main Methods:

  • Protopia accesses multiple protein interaction databases (Transfac, DIP, Hprd, Int-Act, iHop).
  • Results are presented as biological protein names or database codes, visualized as vectors or matrices.
  • Interactive organic graph representation allows for dynamic data handling.
  • Comparison across databases is performed using UniProt codes.

Main Results:

  • The tool successfully locates and integrates information from specified databases.
  • Redundancies in data across different databases are identified.
  • Results are compatible with major network analysis tools for comparative studies.
  • Interactive visualization aids in understanding complex, multi-step protein networks.

Conclusions:

  • Protopia effectively integrates and organizes protein interaction data from various sources.
  • The tool aids in identifying data redundancies, improving data quality.
  • Compatibility with established network analyzers enables broader scientific collaboration and analysis.
  • Enhanced visualization capabilities are crucial for dissecting complex biological networks.