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Ab initio protein structure prediction using chunk-TASSER.

Hongyi Zhou1, Jeffrey Skolnick

  • 1Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.

Biophysical Journal
|May 15, 2007
PubMed
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Chunk-TASSER, a novel ab initio protein structure prediction method, significantly improves accuracy for hard targets by utilizing supersecondary structure chunks and threading templates. This advancement enhances protein modeling where traditional templates are insufficient.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Existing methods like threading struggle with targets lacking identifiable templates.
  • Ab initio methods offer an alternative but often face challenges in accuracy and efficiency.

Purpose of the Study:

  • To develop and evaluate an enhanced ab initio protein structure prediction method, chunk-TASSER.
  • To improve the accuracy of protein structure modeling, particularly for challenging targets.
  • To assess the performance of chunk-TASSER against existing methods like TASSER and SP(3).

Main Methods:

  • Chunk-TASSER employs ab initio folded supersecondary structure chunks and threading templates.

Related Experiment Videos

  • A novel fragment comparison method selects relevant chunks, which are then folded via fragment insertion.
  • Full-length models are built and refined using the TASSER methodology with an optimized force field.

    • Main Results:

    • Chunk-TASSER achieved higher average TM-scores compared to SP(3) and original TASSER across 425 hard targets.
    • For predominantly helical proteins, chunk-TASSER showed marked improvement, with 41.25% of models reaching a TM-score > 0.4.
    • The method demonstrated an 11% (10%) improvement over TASSER for CASP7 targets based on total TM-score.

    Conclusions:

    • Chunk-TASSER represents a significant advancement in ab initio protein structure prediction, especially for difficult targets.
    • The integration of supersecondary structure chunks enhances modeling accuracy where templates are scarce.
    • The fully automated nature of chunk-TASSER enables its application in large-scale proteome analysis.