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== 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 ==

 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. Try different multiple sequence alignment algorithms (MSA) on the PDZ domain sequences to see if they affect the correlation results.
 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 ==
 * Shirley Hui
 * Gary Bader

== Documents ==

== Background Literature ==

=== More General ===
 * The Human and Mouse Complement of SH2 Domain Proteins-Establishing the Boundaries of Phosphotyrosine Signaling, Liu BA, Jablonowski K, Raina M, Arce M, Pawson T and Nash PD, Mol Cell, 2006  Jun 23; 22(6):851-68.

 * Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits, Bhattacharyya RP, Remenyi A, Yeh BJ, Lim WA., Annu Rev Biochem. 2006;75:655-80.
   * attachment:Domains_motifs_scaffolds_Bhattacharyya_et_al_2006.pdf
 * The Structure and Function of Proline Recognition Domains, Zarrinpar A, Bhattacharyya RP, Lim WA., Sci STKE. 2003 Apr 22;2003(179):RE8.
   * attachment:Structure_Function_Pro_Recog_Domains_Zarrinpar_et_al_2003.pdf

=== Specificity Prediction/Inference ===

 * Ab initio prediction of transcription factor targets using structural knowledge, Kaplan T, Friedman N, Margalit H, PLoS Comput Biol. 2005 Jun;1(1):e1. Epub 2005 Jun 24.
   * attachment:Ab_Initio_Prediction_Transcription_Factor_Targets_Using_Structural_Knowlegde_Kaplan_2005.pdf
 * Specificity and robustness in transcription control networks, Sengupta AM, Djordjevic M, Shraiman BI, Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2072-7.
   * attachment:Specificity_robustness_transcription_control_networks_Sengupta_2002.pdf
 * Can we infer peptide recognition specificity mediated by SH3 domains?, Cesareni G, Panni S, Nardelli G, Castagnoli L., FEBS Lett. 2002 Feb 20;513(1):38-44. 
   * attachment:Can_we_infer_PR_specificity_med_by_SH3_Cesareni_et_al_2002.pdf

=== Amino Acid Alphabets ===
 * Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices, Cannata N, Toppo S, Romualdi C, Valle G, Bioinformatics. 2002 Aug;18(8):1102-8.
   * attachment:Simplifying_AA_alphabets_branch_bound_substit_matrices_Cannata_2002.pdf
 * Simplified amino acid alphabets for protein fold recognition and implications for folding, Murphy LR, Wallqvist A, Levy RM, Protein Eng. 2000 Mar;13(3):149-52.
   * attachment:Simplified_AA_alphabets_Murphy_2000.pdf
 * Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases, Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM, Bioinformatics. 2000 Nov;16(11):988-1002.
   * attachment:Iterative_structure_search_for_protein_homologs_Wallqvist_2000.pdf

=== PDZ Related ===
 * PDZ domains-glue and guide., van Ham M, Hendriks W., Mol Biol Rep. 2003 Jun;30(2):69-82.
   * attachment:PDZ_Domains_Glue_and_Guide_2003.pdf
 * PDZ domains: structural modules for protein complex assembly., Hung AY, Sheng M., J Biol Chem. 2002 Feb 22;277(8):5699-702. Epub 2001 Dec 10.
   * attachment:PDZ_Domains_Structural_Modules_2001.pdf
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