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Related Concept Videos

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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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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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

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Protein Function Prediction.

Leonardo Magalhães Cruz1,2, Sheyla Trefflich3, Vinícius Almir Weiss3

  • 1Department of Biochemistry and Molecular Biology, Federal University of Paraná (UFPR), Curitiba, PR, Brazil. leonardo@ufpr.br.

Methods in Molecular Biology (Clifton, N.J.)
|October 8, 2017
PubMed
Summary
This summary is machine-generated.

Predicting protein function is challenging due to diverse biological contexts and novel proteins. This review covers high-throughput sequence analysis strategies like similarity, composition, structure, and interaction for accurate protein function prediction.

Keywords:
BioinformaticsBiological databasesDatabase sequence similarity searchHomologyOntologyPhylogenyProtein domainsProtein familiesProtein function

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Area of Science:

  • * Computational biology and bioinformatics.
  • * Molecular biology and genomics.

Background:

  • * Large-scale omics technologies continually identify novel proteins, increasing the complexity of functional annotation.
  • * Protein function can be context-dependent, requiring sophisticated prediction methods.

Purpose of the Study:

  • * To review current strategies for predicting protein function using high-throughput sequence analysis.
  • * To highlight benchmark tools and knowledge bases for protein function prediction.

Main Methods:

  • * Inference of protein function based on sequence similarity.
  • * Analysis of sequence composition for functional clues.
  • * Utilizing protein structure and protein-protein interaction data.
  • * Exploration of high-throughput sequence analysis techniques.

Main Results:

  • * Discussion of various protein function prediction strategies.
  • * Illustrative workflows demonstrating practical application of prediction tools.
  • * Identification of key benchmark tools and knowledge bases in the field.

Conclusions:

  • * High-throughput sequence analysis offers powerful approaches for predicting protein function.
  • * Integrating multiple data types (sequence, structure, interactions) enhances prediction accuracy.
  • * Continued development of tools and databases is crucial for advancing functional genomics.