Goals

• Predict specificity of peptide recognition domain from the primary amino acid sequence.
• Analyze PDZ, WW and then SH3 domains

Strategy

Status

Tasks

1. Learn SVN, Brain code (ResidueResidueCorrelation)

2. Literature review related to domain specificity (background activity)

3. Run ResidueResidue correlation analysis on PDZ domain data: 1-1 version + try others e.g. 1-2 (Requires: PDZ profiles from Gary)

4. Implement new feature: amino acid groups (learn amino acid groups) + run on PDZ data
5. Think about new PDZ domain features that can be used for prediction.

Ideas

• Use of structural data (PDZ domain structures) (may require homology modeling)
• Use of machine learning methods (SVM for classification and boosting decision tree for interpretable learning model)
• Analysis of correlation within domain and peptide (inter-residue correlation) maybe correspondence analysis

Team

• Shirley Hui
• Gary Bader

Documents

Background Literature

• The Structure and Function of Proline Recognition Domains, Zarrinpar et al., 2003 attachment:Structure_Function_Pro_Recog_Domains_Zarrinpar_et_al_2003.pdf

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