assp

assp assesses residue-by-residue accuracy of consensus secondary structure predictions derived from multiple protein sequence alignments to evaluate agreement between predicted and actual structures within homologous protein families.

Key Features:

• Accuracy Estimation: Estimates the range of expected residue-by-residue accuracies for secondary structure predictions derived from multiple protein sequence alignments.
• Analysis of Structural Families: Leverages analysis of known protein structural families to determine achievable prediction accuracies across homologous proteins.
• Consensus Prediction Evaluation: Provides expected agreement levels between consensus secondary structure predictions and individual protein members within an alignment.
• Domain-specific Validation: Applied to specific protein domains such as annexins, SH2 domains, and SH3 domains to validate predicted accuracy ranges against empirical structures.

Scientific Applications:

• Structural Biology: Enables evaluation of secondary structure prediction reliability to inform protein folding and structure–function studies.
• Protein Engineering: Informs how sequence modifications may affect secondary structure by estimating prediction accuracy and variability.
• Comparative Genomics: Supports comparison of protein secondary structure predictions across species and within homologous families.

Methodology:

Analyzes multiple protein sequence alignments and known protein structural families, using empirical data from known protein structures to determine expected ranges of secondary structure prediction accuracy.