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Domain definition and target classification for CASP7.

Neil D Clarke1, Iakes Ezkurdia, Jürgen Kopp

  • 1Genome Institute of Singapore, 138627 Singapore.

Proteins
|July 27, 2007
PubMed
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The Critical Assessment of protein Structure Prediction (CASP) 7 used experimentally determined protein structures to categorize 123 target domains. Most domains fell into template-based modeling, with some classified as free modeling or high accuracy modeling.

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Experimentally determined protein structures are crucial for assessing protein structure prediction methods.
  • The Critical Assessment of protein Structure Prediction (CASP) is a community-wide experiment for protein structure prediction.
  • CASP assessments categorize targets based on available structural information and prediction methodologies.

Purpose of the Study:

  • To categorize protein target structures from CASP7 for assessment.
  • To define assessment categories based on structural similarity to templates and prediction accuracy.
  • To evaluate the distribution of target domains across different modeling categories in CASP7.

Main Methods:

  • Experimentally determined protein structures were used as targets.

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  • Target structures were divided into domains based on visual inspection and superposition with templates.
  • Domains were classified into "high accuracy modeling," "template-based modeling," and "free modeling" categories.

    • Main Results:

    • Out of 123 target domains in CASP7, 108 were assessed under template-based modeling.
    • Fifteen target domains were classified as free modeling.
    • Twenty-eight domains from template-based modeling were also assessed in the high accuracy category.

    Conclusions:

    • The majority of CASP7 targets relied on template-based modeling approaches.
    • A smaller subset of targets required free modeling, indicating challenges in prediction.
    • The categorization framework allowed for nuanced evaluation of different prediction strategies.