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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.
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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.
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Protein Structure Databases.

Roman A Laskowski1

  • 1European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. roman@ebi.ac.uk.

Methods in Molecular Biology (Clifton, N.J.)
|April 27, 2016
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Summary
This summary is machine-generated.

Protein structure databases offer diverse resources for understanding 3D protein structures and their functions. These databases aid in classifying protein folds, revealing evolutionary links, and analyzing novel protein structures.

Keywords:
CATHESDFold classificationJenaLibOCAPDBPDBePDBsumPfamProtein Data BankProtein structureProtein–ligand interactionsSCOPSecondary structurewwPDB

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Web-based protein structure databases vary widely in type and information.
  • General interest databases include atlases of experimentally determined protein structures.
  • Fold classification databases reveal evolutionary relationships not apparent from sequence alone.

Purpose of the Study:

  • To provide an overview of the landscape of web-based protein structure databases.
  • To highlight the utility of different database types for researchers.
  • To categorize databases based on their content and user focus.

Main Methods:

  • Literature review and synthesis of information on existing protein structure databases.
  • Categorization of databases based on their primary function (e.g., structural atlases, fold classification, fold comparison).
  • Identification of specialized databases for specific user needs.

Main Results:

  • Databases range from general structural atlases with 3D structure and function information to specialized resources.
  • Fold classification databases are crucial for evolutionary analysis.
  • Fold comparison servers are valuable for newly solved structures, especially those with unknown functions.

Conclusions:

  • A diverse ecosystem of protein structure databases exists to support various research needs.
  • Databases facilitate the study of protein 3D structure, function, and evolution.
  • Specialized databases cater to niche research areas, enhancing scientific discovery.