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Protein Networks

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 Networks

Protein Networks

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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Published on: October 19, 2021

Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction

Xianjun Shen, Li Yi, Yang Yi

BMC Bioinformatics

|September 3, 2015

Summary

This study introduces the Adaptive Density Modularity (ADM) algorithm for identifying protein functional modules, improving accuracy by allowing dynamic reassignment of proteins. ADM enhances understanding of cellular organization principles.

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Identifying Protein-protein Interaction Sites Using Peptide Arrays

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Area of Science:

Systems Biology
Bioinformatics
Computational Biology

Background:

Identifying protein functional modules is crucial for understanding cellular organization.
Existing algorithms often suffer from irreversible protein assignments, leading to accumulated errors.
This limits the accuracy and effectiveness of current protein functional module detection methods.

Purpose of the Study:

To develop a novel algorithm for more effective protein functional module detection.
To address the limitations of existing methods regarding protein node reassignment.
To improve the accuracy and reliability of identifying protein functional modules.

Main Methods:

Developed the Adaptive Density Modularity (ADM) algorithm.
Employs adaptive density modularity for network partitioning.
Compares external and internal association degrees for dynamic module evolution.

Main Results:

The ADM algorithm demonstrates superior performance compared to state-of-the-art methods.
Achieved higher accuracy in predicting protein functional modules.
Identified statistically significant modules annotated with Gene Ontology Biological Process terms.

Conclusions:

ADM effectively overcomes the limitations of previous algorithms.
The algorithm provides a more accurate and robust approach to protein functional module detection.
Findings support a deeper understanding of cellular organization principles.