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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 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...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

Protein and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: Jul 11, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

The global trace graph, a novel paradigm for searching protein sequence databases.

Andreas Heger¹, Swapan Mallick, Christopher Wilton

¹Institute of Biotechnology, P.O. Box 56 (Viikinkaari 5), FI-00014 University of Helsinki, Finland.

Bioinformatics (Oxford, England)

|September 8, 2007

Summary

This study introduces a new graph clustering algorithm for protein sequence analysis. It enables the identification of distant protein homologues and functional motifs, improving bioinformatics and genomics research.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Propagating functional annotations to homologous proteins is vital in bioinformatics.
Accurate identification of conserved, non-contiguous sequence motifs is challenging due to evolutionary mutations.

Purpose of the Study:

To develop a novel algorithm for identifying subtle, conserved sequence motifs.
To improve the detection of distant protein homologues and functional signatures.

Main Methods:

A novel graph clustering algorithm is presented.
Protein sequences self-organize into hypothetical multiple sequence alignments.

Main Results:

The algorithm effectively eliminates noise, allowing tracking of non-contiguous motifs between distant homologues.
A new data structure enables faster sequence database searching, outperforming profile-profile comparisons for distant homologues.

Conclusions:

This method enhances the leverage of structural and functional genomics.
It opens new avenues for data mining a comprehensive set of functional signature motifs.