Project Proposal

For an in depth discussion of the project goals and deliverables please read our project proposal.

Supporters

APRI PrioNet

Publications

Papers

Jianjun Zhou, Joerg Sander, Zhipeng Cai, Lusheng Wang, Guohui Lin. "Finding the Nearest Neighbors in Biological Databases Using Less Distance Computations", IEEE/ACM Transactions on Computational Biology and Bioinformatics. To appear.

T. Yamazaki, N. Blinov, D. Wishart, and A. Kovalenko, "Essential Role of Hydration in Aggregation of Misfolded Prion Proteins: Quantification by Molecular Theory of Solvation", Journal of Toxicology and Environmental Health, November 2008.

S Montgomerie, JA Cruz, S Shrivastava, D Arndt, M Berjanskii and DS Wishart. "PROTEUS2: A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation" Nucleic Acids Research 36 (Jul 2008): W202-9.

Y Shi, J Zhou, D Arndt, DS Wishart and GH Lin. "Protein contact order prediction from primary sequences" BMC Bioinformatics 9 (May 2008): 255.

David S. Wishart, David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou and Guohui Lin. "CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data", Nucleic Acids Research, Web server issue, 36: W496 - W502, 2008.

Berjanskii, M.V., Wishart, D.S., The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Research 35 (Web Server issue): W531-537 (2007).

C. Macdonell and P. Lu, "Pragmatics of Virtual Machines for High-Performance Computing: A Quantitative Study of Basic Overheads". In Proc. 2007 High Performance Computing & Simulation Conference (HPCS'07), Prague, Czech Republic, June 4-6, 2007. To appear.

X. Wan and G.-H. Lin. "GASA: A Graph-Based Automated NMR Backbone Resonance Sequential Assignment Program" Journal of Bioinformatics and Computational Biology, 5(2A) (2007), 313-333..

X. Wan and G.-H. Lin. "CISA: Combined NMR Resonance Connectivity Information Determination and Sequential Assignment" IEEE/ACM Transactions on Computational Biology and Bioinformatics 4(3)(2007), 336-348.

P. Drabik, S. Gusarov, and A. Kovalenko, "Microtubule Stability Studied by Three-dimensional Molecular Theory of Solvation", Biophys. J., 92, 394-403 (2007); also Cover of Biophys. J., 15 Jan 2007. Highlighted in Science Daily, 2 Feb 2007.

S. Gusarov, T. Luchko, A. Kovalenko, "HPC parallel implementation of the three-dimensional molecular theory of solvation", patent disclosure to National Research Council - National Institute for Nanotechnology, (2007).

P. Lu, M. Closson, C. Macdonell, P. Nalos, D. Ngo, M. Kan, and M. Lee. "The Trellis Security Infrastructure for Overlay Metacomputers and Bridged Distributed File Systems", Journal of Parallel and Distributed Computing, 66(9):1181--1188, September 2006.

Berjanskii, M.V., Neal, S., Wishart, D.S., "PREDITOR: a web server for predicting protein torsion angle restraints", Nucleic Acids Res. 34(Web Server issue):W63-69 (2006).

Berjanskii, M.V. and Wishart, D.S. "NMR: Prediction of Protein Flexibility" Nature Protocols 1(2): 683-688 (2006). doi:10.1038 /nprot.2006.108

Abstracts and Posters

Blinov, N., Dorosh, L., Wishart, D.S., Kovalenko, A. "Molecular Theory of Solvation: New Insights into Molecular Mechanisms of Misfolding and Aggregation of Prion Proteins" poster presented at PrP Canada 2008, Toronto, ON, Feb. 3-5, 2008.

Wishart D, Arndt D, Berjanskii M, Tang P, Zhou J, Shi Y, Lin G. "CS23D: A Web Server for Rapid Protein Structure Generation Using NMR Chemical Shifts", poster at PrP Canada, Toronto ON, 2008 (PDF)

Lo A, Li L. "Automation of the Dimethylation/Guanidination(2-MEGA) Protocol or Quantification of Chemically Modified Peptides", poster at PrP Canada, Toronto ON, 2008 (PDF)

Yamazaki, T. “Multiscale Theoretical Modeling of Nanochemistry on Solution” presented at the Second NRI-NINT Joint Scientific Workshop, Edmonton, AB (July 2007)

Suriyamongkol B, Semenchenko V, Wishart DS. “Purification and Circular Dichrosim Studies of Recombinant Syrian Hamster Wild Type and Mutant Prion Proteins”, poster presented at the CPI 2007 Meeting, Ottawa ON, (June 2007).

Mongomerie S, Cruz J, Shrivastava S, Arndt D, Berjanskii M, Wishart DS. “Proteus2: A Web Server for Comprehensive Protein Structure Prediction and Structure-Based Annotation”, poster presented at the CPI 2007 Meeting, Ottawa ON, (June 2007).

Zhou J, Shi Y, Lin G, Wishart DS. “A Contact Order Prediction Method”, poster presented at the CPI 2007 Meeting, Ottawa ON, (June 2007).

Zhou GP, Suriyamongkol B, Duggan D, Semenchenko B, Wishart DS. “NMR Characterization of the Reduced Form of he Syrian Hamster Prion”, poster presented at the CPI 2007 Meeting, Ottawa ON, (June 2007).

Reiz, Béla, A. Lo, D. Duggan, B. Suriyamongkol, D. Wishart, L. Li, "Sequencing the prion protein using microwave assisted acid hydrolysis combined with MALDI-MS", presented at PrP Canada, Calgary, AB, Feb 18-21, 2007 [PPT]

B. Suriyamongkol , D. Duggan, V. Semenchenko and D. Wishart, "Over-expression and purification of recombinant murine wild type and mutant prion proteins in E. coli", presented at PrP Canada, Calgary, AB, Feb 18-21, 2007 [PPT]

Zhou, J., Lin, G-H., Shi, Y., Wishart, D.S. "Structure Comparisons between a PrPsc Structure Model and All PDB Structures" presented at PrP Canada 2007, Calgary, AB, Feb. 20-22, 2007

Wishart, D.S., Sundararaj, S., Maiti, R., Coutouly, M.A., Berjanskii, M.V. "Single Spectrum Spectroscopy of Proteins" presented at the 4th Gordon Conference on Computational Aspects of Biomolecular NMR, Aussois, France, Sept. 2006.

Semenchenko, V., Wishart, D.S. “How to Create a Monster. Part I: Birth of Prion”, poster presented at the 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006.

Berjanskii, M.V., Wishart, D.S. “The Random Coil Index and Protein Flexibility”, poster presented at the 6th International Conference of the Canadian Proteomics Initiative, Edmonton, AB, May 10-12, 2006.

Public or Invited Lectures

Wishart, D.S. “Looking Ahead: What’s Next for the Protein Sciences” presented at the CPI07 Conference, Ottawa ON, June 2007 .

Wishart, D.S. “New Approaches for Monitoring Prion Dynamics and Prion Assembly” presented at the Misfolding Diseases: Prion Dynamics and Roles of Chaperones -- CPI06 Satellite Workshop, Edmonton AB, May 9, 2007.

Wishart, D.S. and Berjanskii M.V. "Using Chemical Shifts to Improve Accuracy and Precision in NMR Structures" presented at the 4th Gordon Conference on Computational Aspects of Biomolecular NMR, Aussois, France, Sept. 2006.

Wishart, D.S. "Protein Structure Analysis and Protein-Protein Interactions II" presented at the NHGRI (National Human Genome Research Institute), Bethesda, MD, Oct. 2006.

Wishart, D.S. "A Novel Approach to Characterize Prion Aggregates and the Prion Propagation Complex" presented at PrP Canada 2007, Calgary, AB, Feb. 20, 2007

Wishart, D.S. "What Does PrPc Tell Us About PrPsc?" presented at the Protein Structure Dynamics Working Group - PrP Canada 2007, Calgary, AB, Feb. 22, 2007