Scansite

Scansite predicts protein interactions and identifies short linear sequence motifs and phosphorylation sites to characterize modular signaling domains and signaling networks across proteomes.

Key Features:

• Prediction of Protein Interactions: Predicts interactions using experimental binding data derived from peptide library and phage display experiments, focusing on modular signaling domains.
• Identification of Sequence Motifs: Identifies short sequence motifs recognized by modular signaling domains or phosphorylated by specific kinases and represents them as position-specific scoring matrices (PSSMs) derived from experimental data.
• Database Integration and Proteome-wide Searches: Integrates with SWISS-PROT, TrEMBL, Genpept, and Ensembl for proteome-wide motif and domain searches and, in version 2.0, reduced search run times by approximately 60% compared to its predecessor.
• Motif Customization and Sequence Match Programs: Accepts user-defined motifs, enables dual motif searches combining precompiled Scansite motifs with user-defined matrices, and includes Sequence Match programs that support non-quantitative user-defined motifs.

Scientific Applications:

• Proteome-scale Signaling Network Prediction: Identifies proteins containing motifs associated with signaling domains to predict cell signaling networks within proteomes.
• Kinase-Substrate Specificity: Predicts sequence specificity and identifies optimal substrates for kinases such as cAMP-dependent protein kinase (PKA) and cyclin-dependent kinases (CDKs).
• Candidate Prioritization and Drug Target Identification: Combines motif and domain predictions across proteins and pathways to prioritize putative interactors and potential drug targets in human disease studies.
• Integration with Experimental Data: Facilitates comparison of predictions with experimental results such as two-dimensional gel electrophoresis.

Methodology:

Uses a peptide library–based searching algorithm and position-specific scoring matrices derived from peptide library and phage display experimental binding data, with Sequence Match programs to handle non-quantitative user-defined motifs.