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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Improving the performance of protein threading using insertion/deletion frequency arrays.

Kyle Ellrott1, Jun-Tao Guo, Victor Olman

  • 1Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA. kellrott@csbl.bmb.uga.edu

Journal of Bioinformatics and Computational Biology
|June 25, 2008
PubMed
Summary

Protein evolution shows non-uniform amino acid insertion/deletion probabilities. This study introduces insertion/deletion (indel) frequency arrays (IFAs) to improve protein fold recognition and alignment accuracy, especially for low-sequence-identity proteins.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Protein Structure Prediction

Background:

  • Protein evolution involves deletions and insertions (indels) of amino acids.
  • Current protein fold recognition models often assume uniform indel probabilities.
  • This assumption overlooks the varying importance of amino acids in protein structure maintenance.

Purpose of the Study:

  • To analyze indel patterns in homologous and analogous protein sequences.
  • To develop a method that accounts for non-uniform amino acid indel probabilities.
  • To improve protein alignment accuracy and fold recognition, particularly for proteins with low sequence identity.

Main Methods:

  • Analysis of alignment patterns in homologous and analogous sequences.
  • Determination of insertion/deletion (indel) statistics for individual amino acids.
  • Development and application of insertion/deletion (indel) frequency arrays (IFAs).
  • Integration of IFAs into protein threading algorithms.

Main Results:

  • Identified specific patterns of amino acid insertions and deletions during protein evolution.
  • Quantified the varying probabilities of indels for different amino acids.
  • Demonstrated improved alignment accuracy using IFAs, especially for low-sequence-identity proteins.
  • Showcased enhanced protein fold recognition capabilities with the application of IFAs.

Conclusions:

  • Insertion/deletion (indel) frequency arrays (IFAs) provide a more accurate representation of protein evolution.
  • Accounting for non-uniform indel probabilities significantly enhances protein threading and fold recognition.
  • This approach offers a valuable tool for analyzing protein structure and evolutionary relationships.