James R. Green  PhD (Queen's), P.Eng., SMIEEE
Professor

Web services

	ProtCal (v1)
Desc:	A software package for computing multiple numerical descriptors for protein sequences and structures.
Link:	Download
Reference:	1) Ruiz-Blanco, Y. B., Marrero-Ponce, Y., Paz, W., Green, J.R., "ProtDCal-v1: A Protein Descriptor Generator Software for Data Mining Applications." In preparation. 2) Ruiz-Blanco, Y. B., Marrero-Ponce, Y., Paz, W., García, Y., & Salgado, J. (2013). "Global Stability of Protein Folding from an Empirical Free Energy Function". Journal of Theoretical Biology, 321, 44-53. 3) Ruiz-Blanco, Y. B., García, Y., Sotomayor-Torres, C. M., & Marrero-Ponce, Y. (2010). "New Set of 2D/3D Thermodynamic Indices for Proteins. A Formalism Based on “Molten Globule” Theory." Physics Procedia, 8, 63-72.
	PIPE (3b)
Desc:	Protein-protein interaction prediction engine (PIPE) v3b. Predicts PPIs based on co-occurance of short interaction-mediating protein sequences. Works for multiple species. Has been demonstrated to be the most accurate (highest precision/recall) when operating at high specificities (99.95%) required for high-throughput analysis.
Link:	Goto prediction page
Reference:	1) Pitre, S., Hooshyar, M., Schoenrock, A., Samanfar, B., Jessulat, M., Green, J.R., Dehne, F., Golshani, A., 2012, “Short Co-occurring Polypeptide Regions Can Predict Global Protein Interaction Maps”, (Nature) Scientific Reports, 2:239. 2) Pitre, S., North, C., Alamgir, Md., Jessulat, M., Chan, A., Luo, X., Green, J.R., Dumontier, M., Dehne, F., Golshani, A., 2008, "Global investigation of protein-protein interactions in yeast Saccharomyces cerevisiae using re-occurring short polypeptide sequences", Nucleic Acids Research 36(13):4286-4294. Schoenrock, A., Dehne, F., Green, J.R., Golshani, A., Pitre, S., “MP-PIPE: A Massively Parallel Protein-Protein Interaction Prediction Engine”, ICS’11, Tuscon AZ, USA, May 31-June 4, 11 pages, 2011.
	PIPE-Sites
Desc:	Builds on our PIPE method to also predict the location of protein-protein interaction. More accurate than other contemporary methods when evaluated against experimental data from protein truncation studies (Domino dataset).
Link:	Goto prediction page
Reference:	Amos-Binks, A., Patulea, C., Pitre, S., Schoenrock, A., Gui, Y., Green, J.R., Golshani, A., Dehne, F., 2011, “Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences”, BMC Bioinformatics, 12:225. (This paper was designated as “Highly Accessed”)
	PCI-SS
Desc:	A method of predicting protein secondary structure using a PCI-based classifier and also a consensus method to combine PCI with PSIPRED.
Link:	Goto prediction page
Reference:	1) Green, J.R., Korenberg, M.J., and Aboul-Magd, Md., 2009, "MISO Dynamic Nonlinear Protein Secondary Structure Prediction", BMC Bioinformatics 10:222. 2) J.R. Green, M.J. Korenberg, "Nonlinear system identification provides insight into protein folding", CCECE06, Ottawa, Ontario, 7-10 May, 2006.
	HYPT
Desc:	A prediction server for asparagine and aspartic acid hydroxylation on human proteins using an SVM approach.
Link:	Goto prediction page
Reference:	Manuscript in preparation. Based on the thesis research of Z. Liu and F. Iyuke.
	PCI-SUMO
Desc:	A method of predicting post-translational sumoylation sites on proteins via parallel cascade identification.
Link:	Goto prediction page
Reference:	Green, J.R., Dmochowski G.M., Golshani A., "Prediction of Protein Sumoylation Sites Via Parallel Cascade Identification", CMBEC06, Vancouver, 1-3 June 2006.
	GA-CBE
Desc:	An open source genetic algorithms library for the STI Cell BE processor. Although the STI Cell BE processor is no longer widely used, this project was widely used and has been downloaded more than 500 times.
Link:	Goto project page
Reference:	Green, J.R., Knisely, W., Aghaei, A., "An Extensible Genetic Algorithms Library for the Cell BE Processor", CASCON 2007, Toronto, 22-25 October 2007.
	PCI-ATP
Desc:	A method of predicting ATP- and GTP-binding sites on proteins.
Link:	Coming soon...
Reference:	J.R. Green, M.J. Korenberg, R. David, I. Hunter, "Recognition of Adenosine Triphosphate Binding Sites Using Parallel Cascade System Identification", Ann. Biomed. Eng., vol. 31, pp. 462-470, 2003.