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Related Experiment Videos

Relationship between multiple sequence alignments and quality of protein comparative models.

Domenico Cozzetto1, Anna Tramontano

  • 1Department of Biochemical Sciences, University La Sapienza Rome, Italy.

Proteins
|October 21, 2004
PubMed
Summary

Predicting protein structures with comparative modeling is accurate. A new method evaluates model difficulty using multiple sequence alignments (MSA), improving accuracy assessments for protein structure prediction.

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Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Comparative modeling is a primary method for protein structure prediction due to its accuracy.
  • Model quality assessment is crucial for determining the utility of predicted protein structures.
  • The accuracy of comparative models hinges on template-target divergence and sequence alignment quality.

Purpose of the Study:

  • To introduce a novel method for evaluating the expected difficulty and accuracy of comparative protein models.
  • To assess the impact of multiple sequence alignment (MSA) characteristics on model quality.
  • To analyze trends in comparative modeling accuracy using data from the Critical Assessment of Methods for Structure Prediction (CASP) experiments.

Main Methods:

  • Development of a parameter derived from the MSA to predict comparative model difficulty.

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  • Analysis of CASP experimental data to correlate model accuracy with the derived difficulty parameter.
  • Evaluation of the influence of sequence count and distribution within MSAs on modeling outcomes.

    • Main Results:

    • A method was established to evaluate comparative model difficulty based on MSA properties.
    • The derived parameter effectively predicts expected model accuracy.
    • Improvements in comparative modeling scope and quality between CASP editions are linked to increased sequence availability.

    Conclusions:

    • The developed method provides a priori assessment of comparative modeling quality.
    • Increased availability of homologous protein sequences significantly enhances the accuracy of comparative models.
    • This approach aids in selecting appropriate models for specific applications in structural biology.