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Related Concept Videos

Protein Organization01:24

Protein Organization

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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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Protein Organization01:13

Protein Organization

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Overview
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Protein Networks02:26

Protein Networks

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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.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Protein Families02:47

Protein Families

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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...
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Protein and Protein Structure02:15

Protein and Protein Structure

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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...
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Bioinformatics Tools and Resources for Analyzing Protein Structures.

Jason J Paxman1, Begoña Heras2

  • 1Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Rm 521, LIMS1, Kingsbury Drive, Bundoora, Melbourne, VIC, 3086, Australia.

Methods in Molecular Biology (Clifton, N.J.)
|December 16, 2016
PubMed
Summary
This summary is machine-generated.

Bioinformatics tools help manage and interpret vast protein data. Freely available web resources aid in analyzing protein structures, classification, and function inference for new proteins.

Keywords:
DALIMolProbityPDB-REDOPDBePDBeMotifPDBePISAPDBjPDBsumProFuncProtein Data Bank (PDB)Protein Structure

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The exponential growth of protein sequence and structure data necessitates advanced computational tools.
  • Managing, validating, comparing, and interpreting this data is crucial for biological research.

Purpose of the Study:

  • To review freely available World Wide Web bioinformatics resources.
  • To highlight tools commonly used for protein structure analysis.

Main Methods:

  • Literature review of bioinformatics resources.
  • Focus on web-based tools for protein structure analysis.

Main Results:

  • Identification of key bioinformatics resources for protein data management and analysis.
  • Overview of tools for protein classification and function inference.

Conclusions:

  • Freely accessible web resources are essential for effective protein structure analysis.
  • These tools support the interpretation of large-scale biological data and the discovery of novel protein functions.