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An iterative refinement algorithm for consistency based multiple structural alignment methods.

Yu Chen1, Gordon M Crippen

  • 1Bioinformatics Program, University of Michigan, Ann Arbor, MI 48109, USA.

Bioinformatics (Oxford, England)
|July 1, 2006
PubMed
Summary
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We developed Iterative Refinement of Induced Structural alignment (IRIS) to improve pairwise alignment libraries for multiple structural alignment. This method enhances T-COFFEE performance and produces superior multiple alignments for protein structure prediction.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Multiple Structural Alignment (MSTA) is crucial for tasks like protein fold recognition.
  • Consistency-based MSTA methods rely on Pairwise Alignment Libraries (PAL), which can contain conflicts.
  • Refining PALs before assembly is key to avoiding errors in MSTA.

Purpose of the Study:

  • To introduce an algorithm for refining Pairwise Alignment Libraries (PALs).
  • To propose a novel metric for assessing the consistency of alignment libraries.
  • To enhance the performance of Multiple Structural Alignment (MSTA) methods.

Main Methods:

  • Developed the Iterative Refinement of Induced Structural alignment (IRIS) algorithm.
  • Introduced a new measurement for evaluating library consistency.

Related Experiment Videos

  • Tested IRIS on T-COFFEE and compared results with state-of-the-art MSTA algorithms.

    • Main Results:

    • IRIS significantly improves T-COFFEE performance, especially for less consistent libraries.
    • The refined PALs lead to superior multiple alignment results.
    • IRIS demonstrated consistent performance improvements across multiple benchmarks, including 15 transglycosidases.

    Conclusions:

    • The IRIS algorithm effectively refines Pairwise Alignment Libraries (PALs).
    • This refinement leads to enhanced accuracy in Multiple Structural Alignment (MSTA).
    • IRIS offers a valuable tool for improving protein structure analysis and prediction.