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Related Concept Videos

Protein Families02:47

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 Networks02:26

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 Networks02:26

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 Interfaces02:04

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...
Conservation of Protein Domains Over Different Proteins02:26

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...
Proteomics01:33

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...

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Related Experiment Video

Updated: Jul 14, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

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

Published on: August 16, 2017

Exploiting a list of protein sequences.

Michael C Marden1, Sylvia Dewilde, Laurent Kiger

  • 1Department of Biomedical Sciences, University of Antwerp, B-2610 Antwerp, Belgium. marden@kb.inserm.fr

Gene
|May 29, 2007
PubMed
Summary

This study introduces novel software for analyzing aligned protein sequences, enhancing data visualization with graphical representations and natural parameters like amino acid type and position. Protein engineers can leverage this tool to explore known sequence variants, aiding in protein design and research.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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Last Updated: Jul 14, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

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

Published on: August 16, 2017

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Databases of aligned protein sequences are crucial for understanding protein function and evolution.
  • Existing methods for analyzing sequence data can be cumbersome and lack intuitive visualization.
  • Protein engineers require efficient tools to access and interpret information on protein variants.

Purpose of the Study:

  • To present a software program designed for the effective utilization of aligned protein sequence databases.
  • To introduce graphical representations for improved data overview and analysis.
  • To facilitate the exploration of known protein variants for protein engineering applications.

Main Methods:

  • Development of a software program for protein sequence database exploitation.
  • Implementation of graphical representations alongside traditional sequence lists.
  • Utilization of natural parameters such as amino acid type and sequence position for data analysis.
  • Generation of various plots and 3D representations.

Main Results:

  • The software provides an enhanced overview of sequence data through graphical interfaces.
  • Analysis is facilitated by using intuitive parameters like amino acid type and position.
  • Demonstrated utility with examples from globin sequences and human hemoglobins.
  • The tool effectively displays known sequence variants.

Conclusions:

  • The developed software offers a valuable tool for protein engineers.
  • Graphical representations significantly improve the understanding of complex sequence data.
  • The software aids in identifying and analyzing known protein variants, supporting research and development in protein engineering.