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= A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequences  =
This data is supplementary material for :

''A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequences''

Xiaojian Shao1,2,5, Chris S. H. Tan2,3,5, Courtney Voss4, Shawn S. C. Li4, Naiyang Deng1*, Gary D. Bader2,3*

1. College of Science, China Agricultural University, Beijing, China, 

2. Banting and Best Department of Medical Research, University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada 

3. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

4. Department of Biochemistry, University of Western Ontario, London, Ontario, Canada

5. These authors contributed equally to this work.

* To whom correspondence should be addressed. E-mail: gary.bader@utoronto.ca (GDB); dengnaiyang@cau.edu.cn (NYD)

== Supplemental Materials ==
 * [[attachment:Supplementary Materials.doc]] - Supplementary Notes 1-4 and Figure S1-6 with legends

== Supplemental Tables ==
 * [[attachment:MousePDZdomainpeptideMap.xls|Table S1]] - Quantitative Mouse PDZ Domain-peptide Interaction Matrix
 * [[attachment:SemiSVR_DifferentEncoding.xls|Table S2]] - Performance on Different Encoding
 * [[attachment:SemiSVR_Prediction_MousePDZ.xls|Table S7]] - Predicted Affinity Score for Putative Mouse PDZ Domain-peptide Pairs
 * [[attachment:SemiSVR_Prediction_HumanPDZ.xls|Table S8]] - Predicted Affinity Score for Putative Human PDZ Domain-peptide Pairs

== Semi-quantitative Support Vector Regression Code ==
 * [[attachment:SemiSVR_Code.Zip]] - Matlab code for SemiSVR (compressed). 

== PDZ Sequence ==
 * Mouse PDZ sequence : [[attachment:MousePDZSeq.fasta |MousePDZSequence.fasta]]
 * SemiSVR Predictable Human PDZ Sequence : [[attachment:SemiSVRpredictable_HumanPDZdomain.fa |SemiSVR_Predictable_HumanPDZSequence.fasta]]
 * SemiSVR Predictable Mouse PDZ Sequence : [[attachment:SemiSVRpredictable_MousePDZdomain.fa |SemiSVR_Predictable_MousePDZSequence.fasta ]]