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