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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-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...

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...

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 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: Jul 14, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

MyHits: improvements to an interactive resource for analyzing protein sequences.

Marco Pagni¹, Vassilios Ioannidis, Lorenzo Cerutti

¹Swiss Institute of Bioinformatics (SIB), Vital-IT Group, UNIL-Génopode, CH-1015 Lausanne, Switzerland.

Nucleic Acids Research

|June 5, 2007

Summary

The MyHits web service offers enhanced protein sequence analysis with updated tools and a revamped database. It provides improved usability for researchers studying protein sequences.

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Last Updated: Jul 14, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Published on: July 8, 2025

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

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Published on: July 16, 2017

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:

Bioinformatics
Computational Biology
Molecular Biology

Background:

The MyHits web service has been a resource for protein sequence analysis since 2004.
Continuous development is essential to keep bioinformatics tools relevant and user-friendly.

Purpose of the Study:

To summarize the current status and recent improvements of the MyHits web server.
To highlight newly integrated services and updated functionalities for protein sequence analysis.

Main Methods:

The study details updates to the MyHits web server's user interface and back-end infrastructure.
Key improvements include the integration and updating of analysis tools such as MAFFT, Jacop, Dotlet, Jalview, and ESTScan.
The database schema and API were revamped, and the HitKeeper database engine was separated from the web interface.

Main Results:

The MyHits server now features an improved user interface and enhanced back-end performance.
New and updated tools are available, increasing the service's analytical capabilities.
A restructured database architecture enhances stability and maintainability.

Conclusions:

The MyHits web server remains a valuable integrated resource for protein sequence analysis.
Recent upgrades have significantly improved its usability and expanded its range of services for the scientific community.