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Structure classification-based assessment of CASP3 predictions for the fold recognition targets.

A G Murzin1

  • 1Centre for Protein Engineering, MRC Centre, Cambridge, United Kingdom. agm@mrc-lmb.cam.ac.uk

Proteins
|October 20, 1999
PubMed
Summary

Most protein structure predictions for novel targets in CASP3 (Critical Assessment of protein Structure Prediction) surprisingly resembled known structures. This suggests many novel protein folds were not truly new, impacting fold prediction accuracy assessments.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure prediction

Background:

  • The Critical Assessment of protein Structure Prediction (CASP) is a community-wide experiment to assess protein structure prediction methods.
  • Assessing the accuracy of protein structure prediction is crucial for understanding protein function and evolution.

Purpose of the Study:

  • To evaluate the accuracy of protein structure prediction methods in the fold prediction/recognition category using CASP3 data.
  • To analyze the relationship between predicted and experimentally determined protein structures, particularly for targets with no sequence similarity to known structures.

Main Methods:

  • Analysis of predicted 3D structures against experimental structures for 23 CASP3 targets.
  • Numerical evaluation and classification of predicted models to identify characteristic structural features.

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  • Comparative assessment of predictions to determine the best models for each target, including those with novel folds.

    • Main Results:

    • A significant portion of targets, initially thought to have novel sequences, exhibited structural similarity to known proteins.
    • Eleven of the 23 targets showed distant homology to known structures, and others had substantial similarities.
    • The evaluation process successfully identified correct predictions and assessed the performance of different prediction methods.

    Conclusions:

    • The study highlights the challenge in identifying truly novel protein folds, as many targets share structural similarities with existing ones.
    • The CASP3 results provided insights into the capabilities of various protein structure prediction methods.
    • Accurate fold recognition remains a critical aspect of computational biology and drug discovery.