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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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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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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Phyre2.2: A Community Resource for Template-based Protein Structure Prediction.

Harold R Powell1, Suhail A Islam1, Alessia David1

  • 1Department of Life Sciences, Imperial College London, London SW7 2AZ UK.

Journal of Molecular Biology
|March 26, 2025
PubMed
Summary
This summary is machine-generated.

Phyre2.2 enhances protein structure prediction by integrating AlphaFold models as templates. This updated tool offers a comprehensive protein databank library and improved domain spanning analysis for users.

Keywords:
BioinformaticsHomology modelingPhyre2.2Protein structure prediction

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Template-based modelling (homology modelling) predicts protein structure using known related structures.
  • Recent advances like AlphaFold provide accurate models, even without clear templates.
  • Existing tools require users to manually identify suitable templates.

Purpose of the Study:

  • To introduce Phyre2.2, an enhanced version of the Phyre2 protein structure prediction portal.
  • To integrate AlphaFold models as potential templates within the Phyre2 workflow.
  • To improve the usability and comprehensiveness of protein structure modelling.

Main Methods:

  • Phyre2.2 automatically identifies suitable AlphaFold models to serve as templates for user-submitted protein sequences.
  • The tool searches an expanded template library containing representative structures for all Protein Data Bank (PDB) entries.
  • Ranking algorithms are modified to highlight domain-spanning alignments.

Main Results:

  • Phyre2.2 now incorporates AlphaFold models, expanding template options for protein structure prediction.
  • The template library includes representative apo and holo structures where available.
  • Enhanced hit ranking provides clearer insights into domain organization.

Conclusions:

  • Phyre2.2 offers a more robust and user-friendly approach to protein structure modelling.
  • The integration of AlphaFold models and an expanded template library improves prediction accuracy and scope.
  • Phyre2.2 supports batch processing for proteome-scale analysis and is freely accessible.