A measure of progress in fold recognition?

Area of Science:

• Computational biology
• Structural bioinformatics
• Protein structure prediction

Background:

• The Critical Assessment of protein Structure Prediction (CASP) experiments evaluate protein structure prediction methods.
• Threading methods, also known as template-based modeling, are a key approach in protein structure prediction.
• Assessing progress in fold recognition is crucial for advancing computational biology.

Purpose of the Study:

• To compare the accuracy of protein threading predictions between CASP2 and CASP3.
• To evaluate progress in fold recognition accuracy over successive CASP experiments.
• To determine if threading methods have improved for targets with remote evolutionary relationships.

Main Methods:

• Retrospective analysis of CASP3 threading predictions.
• Application of CASP2 evaluation and assessment criteria to CASP3 data.
• Comparison of model accuracy measures and counts crossing specific thresholds between CASP2 and CASP3.

Main Results:

• Measures of model accuracy were found to be comparable between CASP2 and CASP3.
• The number of accurate models decreased sharply for more difficult targets in both CASP2 and CASP3.
• CASP3 showed an increase in accurate models for medium-difficulty targets, indicating improved performance for remote homology detection.

Conclusions:

• Protein threading accuracy measures are consistent across CASP2 and CASP3.
• Progress in predicting highly difficult protein structures remains limited.
• Threading methods demonstrate enhanced reliability for modeling remote evolutionary relationships in proteins.