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Protein Networks02:26

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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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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 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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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

Yi-Chien Chang1, Zhenjun Hu1, John Rachlin2

  • 1Bioinformatics Program, Boston University, Boston, MA 02215, USA.

Nucleic Acids Research
|December 5, 2015
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Summary
This summary is machine-generated.

The COMBREX database accelerates gene function discovery by linking known and predicted protein functions across microbial genomes. It prioritizes uncharacterized proteins for experimental validation, aiding researchers in understanding biological systems.

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Area of Science:

  • Microbial Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The COMBREX database (COMBREX-DB) serves as a vital online resource for protein function information.
  • It integrates experimentally determined and predicted protein functions, along with associated experimental data.
  • The database supports the COMBREX (COMputational BRidges to EXperiments) initiative to speed up gene function validation.

Purpose of the Study:

  • To describe updates to the COMBREX-DB since its initial publication.
  • To highlight the database's unique features, including its focus on experimental evidence and prioritization of uncharacterized proteins.
  • To present the current scope and capabilities of COMBREX-DB for researchers.

Main Methods:

  • The database aggregates data from over 1000 bacterial and archaeal genomes, encompassing approximately 3.3 million proteins.
  • It includes a prototype recommendation system to identify proteins for informative experimental function determination.
  • Information on experimentally determined function, predicted function, and relationships among proteins of unknown function is curated.

Main Results:

  • COMBREX-DB currently holds comprehensive data on a vast number of microbial proteins.
  • The database emphasizes the documentation of experimental evidence supporting function predictions.
  • A key feature is the prioritization of uncharacterized proteins for experimental investigation.

Conclusions:

  • COMBREX-DB is a unique microbial genomics resource due to its focus on experimental validation and prioritization.
  • The database facilitates the acceleration of gene function discovery in bacteria and archaea.
  • Updates enhance its utility for researchers seeking to validate protein functions and explore microbial diversity.