David S Wishart

Summary

Country: Canada

Publications

  1. 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
  2. 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
  3. pmc 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
  4. pmc 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
  5. pmc 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
  6. pmc 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
  7. pmc 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
  8. pmc 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
  9. pmc 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
  10. pmc 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

Collaborators

Detail Information

Publications80

  1. 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...
  2. 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...
  3. pmc 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...
  4. pmc 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/...
  5. pmc 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...
  6. pmc 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...
  7. pmc 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...
  8. pmc 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...
  9. pmc 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...
  10. pmc 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...
  11. pmc 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...
  12. pmc 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...
  13. pmc 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...
  14. pmc 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...
  15. pmc 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...
  16. pmc 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.)...
  17. pmc 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...
  18. 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...
  19. pmc 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...
  20. pmc 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/...
  21. pmc ECMDB: the E. coli Metabolome Database
    An Chi Guo
    Department of Computing Science, University of Alberta, Edmonton, Alberta T6G 2E8, Canada
    Nucleic Acids Res 41:D625-30. 2013
    ....
  22. pmc METAGENassist: a comprehensive web server for comparative metagenomics
    David Arndt
    Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
    Nucleic Acids Res 40:W88-95. 2012
    ..METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca...
  23. pmc 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...
  24. pmc The human urine metabolome
    Souhaila Bouatra
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    PLoS ONE 8:e73076. 2013
    ..urinemetabolome.ca. ..
  25. pmc YMDB: the Yeast Metabolome Database
    Timothy Jewison
    Department of Computing Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
    Nucleic Acids Res 40:D815-20. 2012
    ....
  26. pmc BacMap: an up-to-date electronic atlas of annotated bacterial genomes
    Joseph Cruz
    Department of Computing Science, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 40:D599-604. 2012
    ..Improved data browsing and searching tools have also been added to allow more facile filtering, sorting and display of the chromosome maps and their contents...
  27. pmc 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...
  28. 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
  29. pmc 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...
  30. pmc DrugBank 3.0: a comprehensive resource for 'omics' research on drugs
    Craig Knox
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    Nucleic Acids Res 39:D1035-41. 2011
    ..0 represents the result of 2 years of manual annotation work aimed at making the database much more useful for a wide range of 'omics' (i.e. pharmacogenomic, pharmacoproteomic, pharmacometabolomic and even pharmacoeconomic) applications...
  31. pmc MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis
    Jianguo Xia
    Department of Biological Sciences, National Institute for Nanotechnology NINT, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 40:W127-33. 2012
    ..A downloadable version of MetaboAnalyst 2.0, along detailed instructions for local installation is now available as well...
  32. doi Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures
    Mark Berjanskii
    Department of Computing Science, University of Alberta, Edmonton, AB, Canada
    J Biomol NMR 53:167-80. 2012
    ..The ResProx web server is available at http://www.resprox.ca...
  33. doi Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach
    Cynthia Stretch
    Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
    J Nutr 142:14-21. 2012
    ..Furthermore, variation in lean and fat mass potentially confounds metabolomic studies attempting to characterize diet or disease conditions. Future studies should account or correct for such variation...
  34. pmc PHAST: a fast phage search tool
    You Zhou
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Nucleic Acids Res 39:W347-52. 2011
    ..PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com)...
  35. pmc 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...
  36. pmc 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 )...
  37. pmc 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...
  38. doi The prion protein binds thiamine
    Rolando Perez-Pineiro
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
    FEBS J 278:4002-14. 2011
    ....
  39. doi 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...
  40. doi 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...
  41. 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...
  42. pmc 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/...
  43. doi Relative and regional stabilities of the hamster, mouse, rabbit, and bovine prion proteins toward urea unfolding assessed by nuclear magnetic resonance and circular dichroism spectroscopies
    Olivier Julien
    Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
    Biochemistry 50:7536-45. 2011
    ..These observations indicate that the regional specific unfolding pattern is the same for the four mammalian prion proteins studied but militate against the idea that PrP(Sc) formation is linked with the global stability of PrP(C)...
  44. pmc 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...
  45. 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...
  46. 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/...
  47. doi Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process
    Trent C Bjorndahl
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E8
    Biochemistry 50:1162-73. 2011
    ..The latter finding represents one of the first examples wherein physiologically accessible conditions (i.e., only low pH) were used to achieve PrP conversion and fibril formation...
  48. pmc 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...
  49. 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
  50. 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...
  51. pmc 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...
  52. 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...
  53. pmc 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...
  54. 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
    ....
  55. 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
    ....
  56. 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...
  57. doi Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers
    Bilkiss B Issack
    National Institute for Nanotechnology, National Research Council, Edmonton, AB, Canada
    Proteins 80:1847-65. 2012
    ..The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins...
  58. doi Resolution-enhanced native acidic gel electrophoresis: a method for resolving, sizing, and quantifying prion protein oligomers
    Carol L Ladner
    Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8
    Anal Biochem 426:54-62. 2012
    ....
  59. pmc Multi-platform characterization of the human cerebrospinal fluid metabolome: a comprehensive and quantitative update
    Rupasri Mandal
    Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB Canada T6G 2E8
    Genome Med 4:38. 2012
    ....
  60. 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...
  61. doi MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets
    Jianguo Xia
    Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
    Bioinformatics 27:2455-6. 2011
    ..These procedures are presented through an intuitive web interface. At the end of each session, a detailed analysis report is generated to facilitate understanding of the results...
  62. pmc The human serum metabolome
    Nikolaos Psychogios
    Department of Computing Science, University of Alberta, Edmonton, Canada
    PLoS ONE 6:e16957. 2011
    ..serummetabolome.ca...
  63. doi 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
    ....
  64. doi Towards automatic metabolomic profiling of high-resolution one-dimensional proton NMR spectra
    Pascal Mercier
    Chenomx Inc, Edmonton, AB, T5K 2J1, Canada
    J Biomol NMR 49:307-23. 2011
    ..Furthermore, the metabolite concentrations exhibit a very high correlation with both simulated and manually-detected values...
  65. 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...
  66. doi 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...
  67. ncbi Introduction to cheminformatics
    David S Wishart
    University of Alberta, Edmonton, Canada
    Curr Protoc Bioinformatics . 2007
    ....
  68. pmc 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...
  69. pmc 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...
  70. doi Metabolomic data processing, analysis, and interpretation using MetaboAnalyst
    Jianguo Xia
    Department of Computing Science, University of Alberta, Alberta, Canada
    Curr Protoc Bioinformatics . 2011
    ..At the end of each session, it produces a detailed analysis report with graphical, tabular, and textual output that summarizes each analytical method used and each result generated...
  71. doi Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst
    Jianguo Xia
    Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
    Nat Protoc 6:743-60. 2011
    ..The complete protocol can be executed in approximately 45 min...
  72. 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...
  73. 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...
  74. 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...
  75. 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...
  76. 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
  77. 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: david.wishart@ualberta.ca...
  78. doi Human Metabolome Database: completing the 'human parts list'
    David S Wishart
    Pharmacogenomics 8:683-6. 2007
  79. 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)...
  80. ncbi Proteomics and the human metabolome project
    David S Wishart
    Expert Rev Proteomics 4:333-5. 2007