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)

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. Try different multiple sequence alignment algorithms (MSA) on the PDZ domain sequences to see if they affect the correlation results.
5. Implement new feature: amino acid groups (learn amino acid groups) + run on PDZ data
6. 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

Tools/Resources

Databases

• [http://www.ensembl.org/ Ensembl]

  • Software system which produces and maintains automatic annotation on selected eukaryotic genomes.

• [http://www.ebi.ac.uk/interpro/ InterPro]

  • Database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.

• [http://www.biomart.org/ BioMart]

  • Query-oriented data management system that simplifies the task of creation and maintenance of advanced query interfaces backed by a relational database. It is particularly suited for providing the 'data mining' like searches of complex descriptive (e.g. biological) data.

Sequence Alignment

Multiple

• [http://www.drive5.com/muscle/ Muscle]

  • MUltiple Sequence Comparison by Log-Expectation.

• [http://www.ebi.ac.uk/clustalw/ ClustalW]

Viewers

• [http://www.jalview.org/ JalView]

  • Multiple alignment viewer/editor written in Java

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.
  • attachment:Human_mouse_complement_of_SH2_domain_proteins_Liu_2006.pdf
• 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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