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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 domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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OverProt: secondary structure consensus for protein families.

Adam Midlik1,2, Ivana Hutařová Vařeková2,3,4, Jan Hutař2

  • 1CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.

Bioinformatics (Oxford, England)
|June 8, 2022
PubMed
Summary

OverProt generates a consensus of protein secondary structures, revealing general folds and variations within protein families. This tool aids in understanding protein family structures and their diversity.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein families share characteristic secondary structures, but individual variations necessitate representative models.
  • A single protein structure is insufficient to capture the diversity within a protein family.

Purpose of the Study:

  • To develop a tool for generating secondary structure consensus for protein families.
  • To visualize general protein folds and variations within families.

Main Methods:

  • The OverProt server computes secondary structure consensus.
  • It provides precomputed results for CATH superfamilies and supports user-defined computations.
  • An interactive viewer displays secondary structure element type, length, frequency, spatial variability, and beta-connectivity.

Main Results:

  • OverProt generates a consensus secondary structure representation for protein families.
  • The server offers precomputed data for CATH superfamilies.
  • An interactive viewer visualizes key structural features and variations.

Conclusions:

  • OverProt effectively represents protein family folds and variations through consensus secondary structures.
  • The tool enhances the understanding of protein structural diversity.
  • It provides valuable insights for structural bioinformatics and computational biology research.