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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 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-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...

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,...

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Related Experiment Video

Updated: Jul 7, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Web-based tools for protein classification.

Costas D Paliakasis¹, Ioannis Michalopoulos, Sophia Kossida

¹Biomedical Research Foundation, Academy of Athens, Athens, Greece.

Methods in Molecular Biology (Clifton, N.J.)

|February 22, 2008

Summary

Proteomics research generates vast data for identifying diagnostic biomarkers and therapeutic targets. This guide explains using web tools to classify proteins and predict their functions from peptide sequences.

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Last Updated: Jul 7, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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

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

Published on: July 16, 2017

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Current proteomics technologies produce extensive datasets, necessitating methods for identifying diagnostic/prognostic biomarkers and therapeutic targets.
Effective classification of proteins into functional families is crucial for understanding their roles and for therapeutic target identification.

Purpose of the Study:

To provide guidelines for exploring peptide sequence data generated by proteomics methodologies.
To utilize web-based tools for predicting protein function and classifying proteins into meaningful families.

Main Methods:

Preprocessing protein sequences to remove internal repeats.
Identifying known protein domains within query sequences.
Utilizing cross-referenced databases and web tools for comparative analysis.

Main Results:

Identification of known protein domains aids in segmenting protein sequences.
Unclassified sequence portions can be analyzed for distant homologues or novel domain discovery.
Web-based tools facilitate the classification of proteins and prediction of their functions.

Conclusions:

Exploring proteomics data with bioinformatics tools enables efficient protein classification and function prediction.
This approach aids in identifying potential biomarkers and therapeutic targets from large-scale proteomics studies.