PhoScan

PhoScan predicts kinase-specific phosphorylation sites in protein sequences using a log-odds ratio scoring approach to identify likely kinase–substrate relationships.

Key Features:

• Log-odds ratio scoring: Uses a log-odds ratio framework to score the likelihood that a peptide is phosphorylated by a specific protein kinase at a given site.
• Feature extraction: Extracts common and kinase-specific sequence features from substrate sequences associated with different protein kinases.
• Experimental-data-derived features: Derives features from analysis of published experimental phosphorylation data.
• Predictive performance: Reports specificity and sensitivity rates above 90% at the kinase-family level based on experimental data.
• Input data source: Applied to predict phosphorylation sites in human proteins sourced from the Swiss-Prot database.
• Kinase families supported: Includes predictions for protein kinase A, cyclin-dependent kinases, and casein kinase 2.

Scientific Applications:

• Phosphorylation site prediction: Predicts putative phosphorylation sites in human proteins from Swiss-Prot.
• Kinase–substrate assignment: Assigns candidate kinases to phosphorylation sites for protein kinase A, cyclin-dependent kinases, and casein kinase 2.
• Phosphorylation dynamics and function studies: Supports investigation of protein function and phosphorylation-mediated signaling events.

Methodology:

Extracts common and kinase-specific features from substrate sequences associated with different protein kinases using published experimental data, and implements a log-odds ratio scoring system to evaluate the likelihood that a peptide is phosphorylated by a specific protein kinase at a particular site within its sequence context.