CleavPredict

CleavPredict predicts potential substrate cleavage sites for 11 human matrix metalloproteinases (MMPs) to support analysis of MMP-mediated proteolytic processes.

Key Features:

• Cleavage site prediction: Predicts potential cleavage sites specific to 11 human MMPs.
• Position weight matrices (PWMs): Uses PWMs derived from statistical analyses of high-throughput phage display experimental data.
• Structural annotation: Provides secondary structure, disordered regions, transmembrane domains, and solvent accessibility information for substrate sites.
• Subcellular context: Provides subcellular localization and co-localization patterns of proteinases and potential substrates.
• Co-expression profiles: Supplies co-expression data for proteinases and substrates.
• Genetic and posttranslational data integration: Integrates experimentally determined single nucleotide polymorphisms (SNPs) and posttranslational modification (PTM) sites in substrates.

Scientific Applications:

• Prediction of MMP substrates: Identification of likely MMP cleavage sites in protein sequences.
• Structural determinant analysis: Assessment of how secondary structure, disorder, transmembrane domains, and solvent accessibility influence MMP-mediated cleavage.
• Spatial dynamics of proteolysis: Analysis of subcellular localization and co-localization to infer where proteolytic events may occur.
• Variant and PTM impact assessment: Evaluation of how SNPs and PTMs may affect substrate recognition and cleavage by MMPs.

Methodology:

Applies position weight matrices (PWMs) derived from statistical analyses of high-throughput phage display experimental data to predict cleavage sites and annotates these sites with secondary structure, disordered regions, transmembrane domains, solvent accessibility, subcellular localization, co-localization, co-expression profiles, and integrates experimentally determined SNP and PTM site data.