Goals
- Predict specificity of peptide recognition domain from the primary amino acid sequence.
- Analyze PDZ, WW and then SH3 domains
Strategy
Status
- [wiki:/Log Status Log]
Tasks
Learn SVN, Brain code (ResidueResidueCorrelation)
- Literature review related to domain specificity (background activity)
Run ResidueResidue correlation analysis on PDZ domain data: 1-1 version + try others e.g. 1-2 (Requires: PDZ profiles from Gary)
- Implement new feature: amino acid groups (learn amino acid groups) + run on PDZ data
- 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