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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

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....

Protein Organization

Protein Organization

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Related Experiment Video

Updated: Mar 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

NAPS: Network Analysis of Protein Structures.

Broto Chakrabarty¹, Nita Parekh²

¹Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India.

Nucleic Acids Research

|May 7, 2016

Summary

This summary is machine-generated.

This study introduces NAPS, a web server for network-based protein structure analysis. NAPS offers a systems approach to understand protein interactions and functions by modeling residue networks.

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Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Traditional protein structure analysis relies on secondary structure and fold arrangement.
Modeling proteins as networks of non-covalent interactions offers a novel systems approach.
Network analysis provides topological insights into complex 3D structures and structure-function relationships.

Purpose of the Study:

To develop and present NAPS, a web server for network-based protein structure analysis.
To facilitate quantitative and qualitative analysis of residue-residue interactions in various protein systems.
To aid in understanding protein folding, domain-domain, and protein-protein interactions.

Main Methods:

Developed a web server, NAPS, for network-based protein structure analysis.
Utilized non-covalent interactions between amino acid residues to construct protein networks.
Enabled user-defined parameters for network construction, including atom type, distance range, and minimal amino acid separation.
Incorporated centrality measures, physicochemical properties, and k-cliques for node selection and analysis.
Provided visualization tools for interacting domains, protein chains, and shortest path lengths between residues.

Main Results:

NAPS facilitates network-based analysis of single chains, protein complexes, modeled structures, and molecular dynamics trajectories.
The server allows for detailed analysis of residue-residue interactions based on user-specified parameters.
NAPS provides various analytical and visualization views for identifying functional residues and interaction mechanisms.

Conclusions:

NAPS offers a powerful platform for exploring protein structure and function through network analysis.
The server aids in elucidating mechanisms of protein folding, domain-domain, and protein-protein interactions.
Network-based analysis provides valuable insights into communication pathways within and between proteins.