Evaluation of template-based models in CASP8 with standard measures

Area of Science:

• Computational biology
• Structural bioinformatics
• Protein structure prediction

Background:

• The Critical Assessment of protein Structure Prediction (CASP) competition has evolved its evaluation strategy for template-based models.
• A standardized procedure has been in place since CASP5 for assessing model quality, scoring, and statistical significance.

Purpose of the Study:

• To describe the detailed workflow for evaluating template-based models in CASP.
• To provide justifications for the choices made in CASP data evaluation.
• To report the analysis of template-based predictions from CASP8.

Main Methods:

• Calculating quality scores for individual protein models.
• Assigning prediction scores based on target result distributions.
• Computing statistical significance of score differences between prediction methods.

Main Results:

• The CASP template-based model evaluation procedure is robust and has been consistently applied.
• Analysis of CASP8 template-based predictions provides insights into prediction method performance.
• The established methods allow for objective comparison and assessment of protein structure prediction accuracy.

Conclusions:

• The CASP evaluation strategy provides a reliable framework for assessing template-based protein model quality.
• The described methodology ensures rigorous and statistically sound comparisons of prediction methods.
• This systematic approach is crucial for advancing the field of protein structure prediction.