#acl BaderLabGroup:read,write,revert,delete All:

== 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)
 1. Literature review related to domain specificity (background activity)
 1. Run ResidueResidue correlation analysis on PDZ domain data: 1-1 version + try others e.g. 1-2  (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

== Team ==

== 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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