D S Wishart

Summary

Affiliation: University of Alberta
Country: Canada

Publications

  1. ncbi Chapter 3: Small molecules and disease
    David S Wishart
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    PLoS Comput Biol 8:e1002805. 2012
  2. ncbi HMDB 3.0--The Human Metabolome Database in 2013
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 41:D801-7. 2013
  3. ncbi SHIFTX2: significantly improved protein chemical shift prediction
    Beomsoo Han
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    J Biomol NMR 50:43-57. 2011
  4. ncbi Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex
    Amanda D Goudie
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    BMC Genomics 9:615. 2008
  5. ncbi Protein contact order prediction from primary sequences
    Yi Shi
    Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada
    BMC Bioinformatics 9:255. 2008
  6. ncbi Improving the accuracy of protein secondary structure prediction using structural alignment
    Scott Montgomerie
    Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    BMC Bioinformatics 7:301. 2006
  7. ncbi MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    BMC Bioinformatics 9:507. 2008
  8. ncbi Circular genome visualization and exploration using CGView
    Paul Stothard
    Department of Biological Sciences and Computing Science, University of Alberta Edmonton, Alberta, Canada T6G 2E8
    Bioinformatics 21:537-9. 2005
  9. ncbi HMDB: a knowledgebase for the human metabolome
    David S Wishart
    Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 37:D603-10. 2009
  10. ncbi DrugBank: a comprehensive resource for in silico drug discovery and exploration
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 34:D668-72. 2006

Collaborators

Detail Information

Publications87

  1. ncbi Chapter 3: Small molecules and disease
    David S Wishart
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    PLoS Comput Biol 8:e1002805. 2012
    ..Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease...
  2. ncbi HMDB 3.0--The Human Metabolome Database in 2013
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 41:D801-7. 2013
    ..This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.)...
  3. ncbi SHIFTX2: significantly improved protein chemical shift prediction
    Beomsoo Han
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    J Biomol NMR 50:43-57. 2011
    ..SHIFTX2 is available both as a standalone program and as a web server ( http://www.shiftx2.ca )...
  4. ncbi Genomic sequence and activity of KS10, a transposable phage of the Burkholderia cepacia complex
    Amanda D Goudie
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    BMC Genomics 9:615. 2008
    ..KS10 was isolated as a prophage of B. cenocepacia K56-2, a clinically relevant strain of the BCC. Our objective was to sequence the genome of this phage and also determine if this prophage encoded any virulence determinants...
  5. ncbi Protein contact order prediction from primary sequences
    Yi Shi
    Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada
    BMC Bioinformatics 9:255. 2008
    ..For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available...
  6. ncbi Improving the accuracy of protein secondary structure prediction using structural alignment
    Scott Montgomerie
    Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    BMC Bioinformatics 7:301. 2006
    ..Indeed, given the large size of the Protein Data Bank (>35,000 sequences), the probability of a newly identified sequence having a structural homologue is actually quite high...
  7. ncbi MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    BMC Bioinformatics 9:507. 2008
    ..However, the lack of dedicated software for this purpose significantly restricts the application of 2D NMR methods to most metabolomic studies...
  8. ncbi Circular genome visualization and exploration using CGView
    Paul Stothard
    Department of Biological Sciences and Computing Science, University of Alberta Edmonton, Alberta, Canada T6G 2E8
    Bioinformatics 21:537-9. 2005
    ..AVAILABILITY: CGView (the standalone application, library or applet), sample input, sample maps and documentation can be obtained from http://wishart.biology.ualberta.ca/cgview/ CONTACT: ...
  9. ncbi HMDB: a knowledgebase for the human metabolome
    David S Wishart
    Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 37:D603-10. 2009
    ..Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users...
  10. ncbi DrugBank: a comprehensive resource for in silico drug discovery and exploration
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 34:D668-72. 2006
    ..DrugBank is available at http://redpoll.pharmacy.ualberta.ca/drugbank/...
  11. ncbi Metabolomics: the principles and potential applications to transplantation
    D S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    Am J Transplant 5:2814-20. 2005
    ....
  12. ncbi DrugBank and its relevance to pharmacogenomics
    David S Wishart
    Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton ABT6G2E8, Canada
    Pharmacogenomics 9:1155-62. 2008
    ..This paper provides a brief overview on DrugBank and how it can facilitate pharmacogenomic research...
  13. ncbi NMR spectroscopy and protein structure determination: applications to drug discovery and development
    David Wishart
    Dept of Biological Sciences, Computing Science and The Faculty of Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Curr Pharm Biotechnol 6:105-20. 2005
    ....
  14. ncbi Dynamic cellular automata: an alternative approach to cellular simulation
    David S Wishart
    Dept of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    In Silico Biol 5:139-61. 2005
    ..An easy-to-use, graphically-based computer program, called SimCell, was developed to perform the DCA simulations described here. It is available at http://wishart.biology.ualberta.ca/SimCell/...
  15. ncbi The human cerebrospinal fluid metabolome
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    J Chromatogr B Analyt Technol Biomed Life Sci 871:164-73. 2008
    ..Tables containing the compounds, concentrations, spectra, protocols and links to disease associations that we have found for the human CSF metabolome are freely available at http://www.csfmetabolome.ca...
  16. ncbi Metabolomics: a complementary tool in renal transplantation
    David S Wishart
    Department of Biological Sciences, University of Alberta, National Research Council, National Institute for Nanotechnology, Edmonton, Alta, Canada
    Contrib Nephrol 160:76-87. 2008
    ..Metabolomics could serve as a good complement to existing proteomic and genomic technologies...
  17. ncbi Metabolomics in monitoring kidney transplants
    David S Wishart
    Department of Biological Sciences, University of Alberta, Canada
    Curr Opin Nephrol Hypertens 15:637-42. 2006
    ..This review describes the basic principles of metabolomics and summarizes a number of recent developments in the use of metabolite biomarkers and metabolomics to monitor kidney transplants...
  18. ncbi HMDB: the Human Metabolome Database
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 35:D521-6. 2007
    ..The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca...
  19. ncbi Current progress in computational metabolomics
    David S Wishart
    Department of Computing Science, Department of Biological Sciences and National Institute for Nanotechnology NRC NINT, University of Alberta, Edmonton Alberta, Canada T6G 2E8
    Brief Bioinform 8:279-93. 2007
    ....
  20. ncbi Advances in metabolite identification
    David S Wishart
    Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8 Canada
    Bioanalysis 3:1769-82. 2011
    ..The strengths and limitations of some of these approaches are discussed along with some of the important trends in metabolite identification...
  21. ncbi Bioinformatics in drug development and assessment
    David S Wishart
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    Drug Metab Rev 37:279-310. 2005
    ..Given the rapid growth in this area and the rapid changes that are taking place, a special emphasis is placed on freely available or Web-accessible resources...
  22. ncbi Computational strategies for metabolite identification in metabolomics
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Bioanalysis 1:1579-96. 2009
    ..The strengths and limitations of these approaches as applied to different analytical technologies (GC-MS, LC-MS and NMR) will be discussed, as will prospects for potential improvements to existing strategies...
  23. ncbi Applications of metabolomics in drug discovery and development
    David S Wishart
    Departments of Biological Science and Computing Science, University of Alberta, Edmonton, Alberta, Canada
    Drugs R D 9:307-22. 2008
    ....
  24. ncbi Improving early drug discovery through ADME modelling: an overview
    David S Wishart
    Department of Biological Science and Computing Science, University of Alberta, Edmonton, AB, Canada
    Drugs R D 8:349-62. 2007
    ..It also discusses what kinds of tools need to be developed, and the importance of integrating ADME data to aid in compound selection during the earliest phases of drug discovery...
  25. ncbi T3DB: a comprehensively annotated database of common toxins and their targets
    Emilia Lim
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    Nucleic Acids Res 38:D781-6. 2010
    ..Potential applications of the T3DB include clinical metabolomics, toxin target prediction, toxicity prediction and toxicology education. The T3DB is available online at http://www.t3db.org...
  26. ncbi Predicting subcellular localization of proteins using machine-learned classifiers
    Z Lu
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada, T6G 2E8
    Bioinformatics 20:547-56. 2004
    ..These are the most accurate subcellular predictors across the widest set of organisms ever published. Our predictors are part of the Proteome Analyst web-service...
  27. ncbi DrugBank: a knowledgebase for drugs, drug actions and drug targets
    David S Wishart
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 36:D901-6. 2008
    ..DrugBank has also significantly improved the power and simplicity of its structure query and text query searches. DrugBank is available at http://www.drugbank.ca...
  28. ncbi The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts
    Mark V Berjanskii
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 35:W531-7. 2007
    ..On average, the correlation between RCI predictions and experimentally obtained motional amplitudes is within the range from 0.77 to 0.82. The server is available at http://wishart.biology.ualberta.ca/rci...
  29. ncbi VADAR: a web server for quantitative evaluation of protein structure quality
    Leigh Willard
    Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2N8, Canada
    Nucleic Acids Res 31:3316-9. 2003
    ..These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar...
  30. ncbi SMPDB: The Small Molecule Pathway Database
    Alex Frolkis
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    Nucleic Acids Res 38:D480-7. 2010
    ..Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca...
  31. ncbi GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images
    Nelson Young
    Department of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8 Canada
    Bioinformatics 20:976-8. 2004
    ....
  32. ncbi The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
    Shan Sundararaj
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2N8, Canada
    Nucleic Acids Res 32:D293-5. 2004
    ..coli (strain K12). The database is self-updating but also supports 'community' annotation, and provides an extensive array of viewing, querying and search options including a powerful, easy-to-use relational data extraction system...
  33. ncbi PPT-DB: the protein property prediction and testing database
    David S Wishart
    Department of Biological Sciences, Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
    Nucleic Acids Res 36:D222-9. 2008
    ..This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca...
  34. ncbi PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
    Dean Cheng
    Department of Computing Science, University of Alberta, Canada
    Nucleic Acids Res 36:W399-405. 2008
    ..Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearch...
  35. ncbi Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
    Duane Szafron
    Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 32:W365-71. 2004
    ..The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA...
  36. ncbi CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
    David S Wishart
    Department of Computing Science, Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology NINT, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 36:W496-502. 2008
    ..The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds. CS23D is accessible at http://www.cs23d.ca...
  37. ncbi BacMap: an interactive picture atlas of annotated bacterial genomes
    Paul Stothard
    Department of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 33:D317-20. 2005
    ..Each genome map is searchable via a local BLAST search and a gene name/synonym search. BacMap is freely available at http://wishart.biology.ualberta.ca/BacMap/...
  38. ncbi PlasMapper: a web server for drawing and auto-annotating plasmid maps
    Xiaoli Dong
    Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 32:W660-4. 2004
    ..The images and textual output are of sufficient quality that they may be used directly in publications or presentations. The PlasMapper web server is freely accessible at http://wishart.biology.ualberta.ca/PlasMapper...
  39. ncbi Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment
    P M Hooper
    Department of Mathematical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2G1
    Bioinformatics 16:425-38. 2000
    ..Improvements in accuracy and speed are needed to deal with the increasing volume of data from large scale sequencing projects...
  40. ncbi The BioTools Suite. A comprehensive suite of platform-independent bioinformatics tools
    D S Wishart
    Faculty of Pharmacy and Pharmaceutical Sciences, 3118 Dentistry Pharmacy Building, University of Alberta, Edmonton, Alberta, Canada T6G 2N8
    Mol Biotechnol 19:59-77. 2001
    ..This article describes the key features, recent changes, and general operation of all three programs...
  41. ncbi Solid phase synthesis of acylglycine human metabolites
    Rolando Perez-Pineiro
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    Bioorg Med Chem Lett 19:6706-8. 2009
    ..The developed methodology facilitates the preparation of several structurally-diverse acylglycines with high yields and purity...
  42. ncbi MetaboAnalyst: a web server for metabolomic data analysis and interpretation
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton AB T6G 2E8, Canada
    Nucleic Acids Res 37:W652-60. 2009
    ..MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. MetaboAnalyst is accessible at http://www.metaboanalyst.ca...
  43. ncbi Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping
    Jung Soh
    Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, AB, Canada
    Int J Nanomedicine 4:79-89. 2009
    ....
  44. ncbi Identifying putative drug targets and potential drug leads: starting points for virtual screening and docking
    David S Wishart
    Departmentsof Computing Science, University of Alberta, Edmonton, Canada
    Methods Mol Biol 443:333-51. 2008
    ..This chapter is intended to illustrate how bioinformatics and cheminformatics can work synergistically to help provide the necessary inputs for computer-aided drug design...
  45. ncbi GeNMR: a web server for rapid NMR-based protein structure determination
    Mark Berjanskii
    Department of Computing Science, University of Alberta and National Research Council, National Institute for Nanotechnology, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 37:W670-7. 2009
    ..GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca...
  46. ncbi In silico drug exploration and discovery using DrugBank
    David S Wishart
    University of Alberta and the National Institute of Nanotechnology NINT National Research Council, Edmonton, Alberta, Canada
    Curr Protoc Bioinformatics . 2007
    ..The intent of this unit is to give readers some introduction into the field of cheminformatics (the study of chemical information) and to show how cheminformatics can be seamlessly integrated into the field of bioinformatics...
  47. ncbi Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors
    Rolando Perez-Pineiro
    Department of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
    J Med Chem 52:1670-80. 2009
    ..Assays measuring the inhibiting effect of these compounds on T. cruzi and T. brucei TryR confirm their potential for further rational optimization...
  48. ncbi Drug-target discovery in silico: using the web to identify novel molecular targets for drug action
    David S Wishart
    University of Alberta, Canada
    SEB Exp Biol Ser 58:145-76. 2007
  49. ncbi RefDB: a database of uniformly referenced protein chemical shifts
    Haiyan Zhang
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2N8, Canada
    J Biomol NMR 25:173-95. 2003
    ..RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website...
  50. ncbi SuperPose: a simple server for sophisticated structural superposition
    Rajarshi Maiti
    Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 32:W590-4. 2004
    ..The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/...
  51. ncbi Computational systems biology in drug discovery and development: methods and applications
    Wayne Materi
    National Research Council, National Institute for Nanotechnology NINT Edmonton, Alberta, Canada T6G 2E8
    Drug Discov Today 12:295-303. 2007
    ..This review provides a brief summary and an assessment of most of these approaches. It also provides examples of how these methods are being used to facilitate drug discovery and development...
  52. ncbi BASys: a web server for automated bacterial genome annotation
    Gary H Van Domselaar
    Department of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
    Nucleic Acids Res 33:W455-9. 2005
    ..The BASys server and databases can also be downloaded and run locally. BASys is accessible at http://wishart.biology.ualberta.ca/basys...
  53. ncbi PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
    Paul Lu
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 33:D147-53. 2005
    ..Third, the whole of PA-GOSUB can be downloaded in either FASTA or comma-separated values (CSV) formats...
  54. ncbi PREDITOR: a web server for predicting protein torsion angle restraints
    Mark V Berjanskii
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    Nucleic Acids Res 34:W63-9. 2006
    ..The PREDITOR website is located at: http://wishart.biology.ualberta.ca/preditor...
  55. ncbi Protein chemical shift analysis: a practical guide
    D S Wishart
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada
    Biochem Cell Biol 76:153-63. 1998
    ....
  56. ncbi MovieMaker: a web server for rapid rendering of protein motions and interactions
    Rajarshi Maiti
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 33:W358-62. 2005
    ..MovieMaker is accessible at http://wishart.biology.ualberta.ca/moviemaker...
  57. ncbi PROSESS: a protein structure evaluation suite and server
    Mark Berjanskii
    Department of Computing Science, University of Alberta, Canada
    Nucleic Acids Res 38:W633-40. 2010
    ..PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca...
  58. ncbi MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    Nucleic Acids Res 38:W71-7. 2010
    ..MSEA has the potential to help users identify obvious as well as 'subtle but coordinated' changes among a group of related metabolites that may go undetected with conventional approaches. MSEA is freely available at http://www.msea.ca...
  59. ncbi Structural and functional characterization of a thioredoxin-like protein (Mt0807) from Methanobacterium thermoautotrophicum
    Godwin Y Amegbey
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada T6G 2N8
    Biochemistry 42:8001-10. 2003
    ..thermoautotrophicum, while Mt0895 plays a minor or supportive role. We also suggest that these two molecules (Mt0807 and Mt0895) may represent a group of ancient proteins that were ancestral to both thioredoxins and glutaredoxins...
  60. ncbi PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
    Scott Montgomerie
    Department of Computing Science and Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology NINT, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 36:W202-9. 2008
    ..2 A RMSD). The average PROTEUS2 prediction takes approximately 3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2...
  61. ncbi Accurate prediction of protein torsion angles using chemical shifts and sequence homology
    Stephen Neal
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    Magn Reson Chem 44:S158-67. 2006
    ..SHIFTOR is available as a freely accessible web server at http://wishart.biology.ualberta.ca/shiftor...
  62. ncbi Structural domains and main-chain flexibility in prion proteins
    N Blinov
    National Institute for Nanotechnology NRC, Edmonton, Alberta T6G 2M9, Canada
    Biochemistry 48:1488-97. 2009
    ..We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins...
  63. ncbi Myxoma virus and malignant rabbit fibroma virus encode a serpin-like protein important for virus virulence
    C Upton
    Department of Biochemistry, University of Alberta, Edmonton, Canada
    Virology 179:618-31. 1990
    ....
  64. ncbi Dynamic relationships among type IIa bacteriocins: temperature effects on antimicrobial activity and on structure of the C-terminal amphipathic alpha helix as a receptor-binding region
    Kamaljit Kaur
    Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
    Biochemistry 43:9009-20. 2004
    ..This study assists in the understanding of structure-activity relationships in type IIa bacteriocins and demonstrates the importance of the conserved C-terminal amphipathic alpha helix for activity...
  65. ncbi Application of the random coil index to studying protein flexibility
    Mark V Berjanskii
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    J Biomol NMR 40:31-48. 2008
    ..The server is available at http://wishart.biology.ualberta.ca/rci...
  66. ncbi Exploring human metabolites using the human metabolome database
    Ian J Forsythe
    Genome Alberta, Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
    Curr Protoc Bioinformatics . 2009
    ....
  67. ncbi NMR: prediction of protein flexibility
    Mark Berjanskii
    Department of Computing Science, 2-21 Athabasca Hall, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
    Nat Protoc 1:683-8. 2006
    ..When chemical shift assignments are available, protein flexibility parameters, such as S2 and RMSF, can be calculated within 1-2 h using a spreadsheet program...
  68. ncbi Introduction to cheminformatics
    David S Wishart
    University of Alberta, Edmonton, Canada
    Curr Protoc Bioinformatics . 2007
    ....
  69. ncbi MetPA: a web-based metabolomics tool for pathway analysis and visualization
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    Bioinformatics 26:2342-4. 2010
    ..MetPA currently enables analysis and visualization of 874 metabolic pathways, covering 11 common model organisms. AVAILABILITY: Freely available at http://metpa.metabolomics.ca...
  70. ncbi Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts
    Stephen Neal
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2N8, Canada
    J Biomol NMR 26:215-40. 2003
    ..SHIFTX is freely available as a web server at http://redpoll.pharmacy.ualberta.ca...
  71. ncbi 1H, 13C and 15N chemical shift referencing in biomolecular NMR
    D S Wishart
    Department of Biochemistry, University of Alberta, Edmonton, Canada
    J Biomol NMR 6:135-40. 1995
    ....
  72. ncbi Production of an anti-prostate-specific antigen single-chain antibody fragment from Pichia pastoris
    Y Wang
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, T6G 2N8, Canada
    Protein Expr Purif 23:419-25. 2001
    ..3 antibody. The protocol described here provides a quick and convenient route to prepare large quantities of very pure anti-PSA antibody fragments (15-20 mg/L culture medium) for detailed structural and biophysical characterization...
  73. ncbi Identification of a novel archaebacterial thioredoxin: determination of function through structure
    Sudeepa Bhattacharyya
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
    Biochemistry 41:4760-70. 2002
    ..On the basis of the results presented here, we predict that these small proteins are all members of a new class of truncated thioredoxins...
  74. ncbi Solution structures of reduced and oxidized bacteriophage T4 glutaredoxin
    Yunjun Wang
    Department of Computing Science and Biological Sciences, University of Alberta, Edmonton, T6G 2E8, Canada
    J Biomol NMR 29:85-90. 2004
  75. ncbi A simple method to predict protein flexibility using secondary chemical shifts
    Mark V Berjanskii
    Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    J Am Chem Soc 127:14970-1. 2005
    ..Further, we show that this chemical shift method is able to quantitatively predict per-residue RMSD values (from both MD simulations and NMR structural ensembles) as well as model-free backbone order parameters...
  76. ncbi NMR solution structure of the precursor for carnobacteriocin B2, an antimicrobial peptide from Carnobacterium piscicola
    Tara Sprules
    Department of Chemistry, University of Alberta, Edmonton, AB, Canada
    Eur J Biochem 271:1748-56. 2004
    ..The latter effect may assist the producing cell in avoiding the toxic effects of the bacteriocin. This is the first 3D structure determined for a prebacteriocin from lactic acid bacteria...
  77. ncbi Proteomics and the human metabolome project
    David S Wishart
    Expert Rev Proteomics 4:333-5. 2007
  78. ncbi NMR solution structures of the apo and peptide-inhibited human rhinovirus 3C protease (Serotype 14): structural and dynamic comparison
    Trent C Bjorndahl
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
    Biochemistry 46:12945-58. 2007
    ..Furthermore, a number of residues exhibited exchange-broadened amide NMR signals in the apo state compared to the inhibited state. The majority of these residues are associated with proteolytic substrate interaction...
  79. ncbi Automated bacterial genome analysis and annotation
    Paul Stothard
    Departments of Biological Sciences and Computing Science, University of Alberta, Alberta, Canada
    Curr Opin Microbiol 9:505-10. 2006
    ..The combined challenge of revising existing annotations and extracting useful information from the flood of new genome sequences will necessitate more reliance on completely automated systems...
  80. ncbi Probing the structural determinants of type II' beta-turn formation in peptides and proteins
    Alan C Gibbs
    Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2N8
    J Am Chem Soc 124:1203-13. 2002
    ..We believe this information could be particularly useful for the prediction of beta-turn propensity, the development of peptide-based drugs, and the de novo design of peptides, proteins, and peptidyl mimetics...
  81. ncbi Human Metabolome Database: completing the 'human parts list'
    David S Wishart
    Pharmacogenomics 8:683-6. 2007
  82. ncbi Solution Structure of MTH0776 from Methanobacterium thermoautotrophicum
    Godwin Amegbey
    Department of Computing Science and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E8
    J Biomol NMR 33:51-6. 2005
  83. ncbi A simple method to adjust inconsistently referenced 13C and 15N chemical shift assignments of proteins
    Yunjun Wang
    Mesolight LLC, Fayetteville, AR, 7270, USA
    J Biomol NMR 31:143-8. 2005
    ..Furthermore, this protocol appears to improve the accuracy of chemical shift-derived secondary structural identification, and has been formally incorporated into a computer program called PSSI (http//www.pronmr.com)...
  84. ncbi Identification of novel and known oocyte-specific genes using complementary DNA subtraction and microarray analysis in three different species
    Maud Vallée
    Centre de Recherche en Biologie de la Reproduction, Departement des Sciences Animales, Universite Laval, Quebec, Canada
    Biol Reprod 73:63-71. 2005
    ..Further characterization of these novel oocyte-specific genes will lead to a better understanding of the molecular mechanisms related to the unique functions found in the oocyte...
  85. ncbi Complete 1H, 13C and 15N NMR assignments of MTH0776 from Methanobacterium thermoautotrophicum
    Godwin Amegbey
    J Biomol NMR 30:459-60. 2004
  86. ncbi Backbone 1H, 15N and 13C assignments for the human rhinovirus 3C protease (serotype 14)
    Trent C Bjorndahl
    J Biomol NMR 26:85-6. 2003
  87. ncbi Synthesis and evaluation of keto-glutamine analogues as potent inhibitors of severe acute respiratory syndrome 3CLpro
    Rajendra P Jain
    Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
    J Med Chem 47:6113-6. 2004
    ..Attachment of tripeptide (Ac-Val-Thr-Leu) to these glutamine-based "warheads" generated significantly better inhibitors (4a-c, 8a-d) with IC(50) values ranging from 0.60 to 70 microM...