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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

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-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 polypeptide...

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 polypeptide...

Ligand Binding Sites

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 6, 2026

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

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

Published on: March 3, 2015

Discovering pathways by orienting edges in protein interaction networks.

Anthony Gitter¹, Judith Klein-Seetharaman, Anupam Gupta

¹Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA.

Nucleic Acids Research

|November 27, 2010

Summary

This study introduces algorithms to orient protein interaction edges, enabling the discovery of directed signaling pathways. The new method significantly outperforms existing techniques in identifying known and novel signaling cascades.

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

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Published on: March 3, 2015

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
Computational Biology
Bioinformatics

Background:

Modern experimental techniques identify cellular interaction proteins.
Reconstructing directed signaling pathways from undirected protein interaction data is challenging.
Existing methods struggle to orient edges in protein interaction networks.

Purpose of the Study:

To develop methods for orienting protein interaction edges.
To discover high-confidence signaling pathways from experimental data.
To improve the prediction of cellular signaling networks.

Main Methods:

Formalized the edge orientation problem in weighted protein interaction graphs.
Developed three approximation algorithms using weighted Boolean satisfiability solvers and probabilistic assignments.
Applied algorithms to identify pathways in yeast.

Main Results:

The developed algorithms successfully oriented protein interaction edges.
Recovered twice as many known signaling cascades compared to a recent unoriented prediction technique.
Identified over 13 times more pathways than an existing network orientation algorithm.
Discovered novel pathway components extending current signaling databases.

Conclusions:

The proposed algorithms effectively orient protein interaction edges for pathway discovery.
This approach enhances the identification of known and novel signaling pathways.
The method offers a significant advancement in computational systems biology for understanding cellular signaling.