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Related Concept Videos

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...
Protein Families02:47

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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 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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: Jun 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

ProteinArchitect: protein evolution above the sequence level.

Matthias Haimel1, Karin Pröll, Michael Rebhan

  • 1Department of Bioinformatics, Upper Austrian University of Applied Sciences, Hagenberg, Austria.

Plos One
|July 16, 2009
PubMed
Summary
This summary is machine-generated.

ProteinArchitect offers a visual comparison of protein features beyond sequence, aiding in functional hypothesis generation for millions of new proteins. This tool helps analyze protein architecture, including domains and disorder, for evolutionary insights.

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Related Experiment Videos

Last Updated: Jun 21, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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Published on: July 16, 2017

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

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Science

Background:

  • Protein function is governed by higher-order features like domains and motifs, not just sequence.
  • Existing tools often focus on sequence similarity, limiting functional insights for novel proteins.
  • Protein architecture, visualized as domain organization, aids in comparing protein structures.

Purpose of the Study:

  • To introduce a visual approach and web server for protein comparison beyond sequence level.
  • To enable comparison of secondary structure, transmembrane domains, intrinsic disorder, and PFAM domains.
  • To facilitate hypothesis generation for protein function using conserved features.

Main Methods:

  • Developed an information-rich, compact visualization of protein features.
  • Extended the domain organization cartoon concept for broader feature representation.
  • Created a public web server (www.proteinarchitect.net) and released the code.

Main Results:

  • The ProteinArchitect server allows visual comparison of diverse protein features.
  • Enables analysis of secondary structure, transmembrane domains, and intrinsic disorder.
  • Facilitates identification of conserved features outside globular regions.

Conclusions:

  • Visualizing protein architecture aids in assessing similarity search relevance.
  • Useful for discovering subgroups within protein families and superfamilies.
  • Helps generate testable hypotheses for protein function, even for distant homologs.