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Related Concept Videos

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.
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,...
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Protein Networks02:26

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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...
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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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Proteomics01:33

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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.
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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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Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions
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Protein Bioinformatics Databases and Resources.

Chuming Chen1, Hongzhan Huang2, Cathy H Wu3,4

  • 1Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA. chenc@udel.edu.

Methods in Molecular Biology (Clifton, N.J.)
|February 3, 2017
PubMed
Summary
This summary is machine-generated.

This review categorizes major protein bioinformatics databases to aid researchers. It also explores future challenges and opportunities for protein data resources in the Big Data era.

Keywords:
Big dataBioinformaticsData analyticsData integrationDatabasePTMPathwayProtein familyProtein functionProtein interactionProtein mutationProtein sequenceProtein structureProteomics

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • Numerous protein data repositories exist to aid research.
  • Effective management and discovery of biological knowledge are crucial.
  • Researchers need efficient ways to find relevant protein informatics resources.

Purpose of the Study:

  • To provide a comprehensive review and categorization of major protein bioinformatics databases.
  • To guide researchers in selecting appropriate resources for their work.
  • To discuss the future development of protein databases in the context of Big Data.

Main Methods:

  • Systematic review of publicly available protein data repositories.
  • Categorization and description of identified bioinformatics databases.
  • Analysis of current trends and future prospects in protein data resource development.

Main Results:

  • A categorized overview of key protein bioinformatics databases is presented.
  • The review facilitates easier access to essential protein-related information.
  • Identified challenges and opportunities for next-generation databases are outlined.

Conclusions:

  • A structured approach to protein bioinformatics databases is essential for research.
  • Future protein database development must address data integration and analytics.
  • The Big Data era presents both challenges and significant opportunities for protein informatics.