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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,...

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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 Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

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: May 16, 2026

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

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

Published on: July 16, 2017

eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy

Florian Heinke¹, Stefan Schildbach, Daniel Stockmann

¹Department of Mathematics, University of Applied Sciences Mittweida, Mittweida, Saxony, Technikumplatz 17, D-09648, Germany. florian.heinke@hs-mittweida.de

Nucleic Acids Research

|November 20, 2012

Summary

Understanding protein structure and function is challenging. A new tool, eProS, uses protein energy profiles to reveal these features, aiding molecular system analysis.

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Last Updated: May 16, 2026

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

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Published on: July 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Determining structural and functional features of novel proteins is critical for understanding molecular mechanisms.
Protein energy profiles, derived from coarse-grained models, offer a novel approach to analyze protein mechanics and dynamics.
These profiles can be computed from structures or predicted from sequences.

Purpose of the Study:

To introduce eProS, a comprehensive database and toolbox for analyzing protein energy profiles.
To facilitate the investigation of sequence-structure-function relationships.
To aid in understanding molecular system dynamics.

Main Methods:

Development of the eProS (energy profile suite) database containing ~76,000 pre-calculated energy profiles.
Implementation of a toolbox for calculating energy profiles from protein structures or sequences.
Features for browsing, visualization, alignment, and comparison of energy profiles against the database.

Main Results:

eProS provides a large repository of pre-calculated energy profiles.
The suite enables direct calculation or prediction of energy profiles.
Comparison tools identify similar energy profiles, suggesting potential structural and functional relationships.

Conclusions:

eProS is a valuable resource for structure biology, offering novel insights through energy profile analysis.
The database and tools aid in uncovering protein mechanics, dynamics, and functional relationships.
Integration with external annotations enhances the biological relevance of identified correspondences.