Assessment of predictions submitted for the CASP7 function prediction category

Area of Science:

• Computational biology
• Bioinformatics
• Structural biology

Background:

• The Critical Assessment of Protein Structure Prediction (CASP) is a community-wide effort to assess protein structure prediction methods.
• CASP7 included a function prediction category evaluating Gene Ontology (GO) terms, Enzyme Commission (EC) numbers, and ligand binding site residues.

Purpose of the Study:

• To provide a comprehensive overview of the CASP7 function prediction category.
• To assess the effectiveness of different functional prediction categories for blind evaluation.
• To identify areas for improvement in future CASP assessments.

Main Methods:

• Predictions for GO molecular function terms and EC numbers were assessed.
• Ligand binding site residue predictions were evaluated.
• The feasibility of blind assessment for each category was analyzed.

Main Results:

• Assessing GO terms and EC numbers was challenging due to pre-existing data, making predictions non-blind.
• Despite non-blind conditions, performance differences among groups were observed for GO terms.
• The ligand binding residue category allowed for blind assessment but received few predictions.

Conclusions:

• There is a clear need for improved blind assessment categories in protein function prediction.
• Focusing on ligand binding site prediction offers the most viable approach for true blind evaluation in CASP.
• Future CASP experiments should prioritize developing more effective blind functional prediction categories.