People

Grad Studies Opportunities

Projects

• The Human Metabolome Project
• The Human Metabolite Database
• The Human Metabolite Library
  
• Protein-Based Drug Targeting and Medical Diagnostics:
  the development of new methods for the targeted delivery of drugs or diagnostic agents using peptide or protein-based vehicles;
• NMR Technology Development:
  the development novel applications in NMR spectroscopy to facilitate structure-aided drug design;
• Pharmaceutical Bioinformatics:
  the development of innovative bioinformatics and modeling software for improved protein/peptide analysis.

Usage Statistics For Our Web Servers

Usage statistics for our servers are analyzed by The Webalizer.

• Check the Usage Statistics for Redpoll Server
• Check the Usage Statistics for Canadian Bioinformatics Help Desk
• Check the Usage Statistics for Wishart Server

Programs and Databases (Web Servers)

• HMDB
  The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database currently contains nearly 2500 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 5500 protein (and DNA) sequences are linked to these metabolite entries.
• PPT-DB
  The PPT-DB is a database of databases. It houses more than 20 carefully curated databases, each of which contain commonly predicted protein property information.
• CS23D
  CS23D is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.
• CCDB Database (CCDB)
  A comprehensive E.coli specific database, containing genomic, proteomic and metabolomic information.
• PROTEUS
  A universal protein structure prediction server that will take any query protein sequence and predict the secondary structure, membrane spanning helices, membrane spanning beta strands, signal peptides, and 3D structures.
• PROTEUS2
  PROTEUS2 is a protein structure prediction and structure-based annotation software application that provides secondary structure, and if possible, tertiary structure information about one or more query seqeunces. Available as both a web server and a standalone command line interface application, PROTEUS2 creates a single prediction pipeline consisting of: 1) signal peptide prediction, 2) transmembrane helix prediction, 3) transmembrane -barrel prediction, 4) secondary structure prediction (for soluble proteins), and 5) homology modeling (i.e. 3D structure generation). Predictions are performed using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, neural nets, and up-to-date databases of known secondary structure assignments.
• BASys
  BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
• BacMap
  An interactive visual database containing all publicly available bacterial genomes. A fully labeled and zoomable genome map is provided for each genome. Sequence and text queries can be used to identify genes of interest, or maps can be navigated using a simple interface. BacMap is designed to serve as an intuitive and convenient tool for identifying orthologues and paralogues, studying operon conservation, and determining gene function.
• MovieMaker
  MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics.
• DrugBank Database
  A database for drug structure and functional information.
• PlasMapper
  A web server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.
• SuperPose
  SuperPose is a protein superposition server.
• GelScape
  GelScape is a web-based gel viewing and annotation system.
• SHIFTX Web Server
  A web server that predicts ¹H, ¹³C, and ¹⁵N protein chemical shifts using the 3D structure (PDB coordinates) of the protein of interest.
• SHIFTY Web Server
  A web server for predicting protein chemical shifts using only amino acid sequence information.
• SHIFTZ Web Server
  A web server that calculates ¹H, ¹³C, and ¹⁵N backbone chemical shifts of peptides and proteins using only their sequence and backbone dihedral angles as input.
• SIMPRED Web Server
  A web server that predicts ¹H, ¹³C and ¹⁵N backbone chemical shifts of peptides and proteins using only the amino acid sequence and the predicted (known) secondary structure as input.
• SHIFTCOR Web Server
  A web server that compares, corrects and references chemical shift assignments using 3D structure (PDB coordinates) of assigned proteins.
• SHIFTOR Web Server
  A web server that predicts protein backbone dihedral angles (phi and psi) from observed ¹H, ¹³C and ¹⁵N chemical shifts.
• SSASS Web Server
  A web server that allows you to obtain sequential assignments and a 3D structure for your favorite protein using only its sequence and at least one (HNCACB) peak list as input.
• THRIFTY Web Server
  A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding chemical shift assignments
• HOMODELLER Web Server
  A web server that rapidly generates 3D protein structures (PDB coordinates) from their corresponding protein sequence.
• RefDB Web-Enabled Database
  The Re-referenced Protein Chemical Shift Database (RefDB) is a database of carefully corrected and re-referenced chemical shifts, derived from the BioMagResBank.
• PEPMAKE Web Server
  A web server that generates a PDB coordinate file for a polypeptide using only the sequence and backbone dihedral angles as input.
• VADAR Web Server
  VADAR (Volume, Area, Dihedral Angle Reporter), this web server quantitively evaluates protein structures using their PDB coordinates.
• PolySearch Web Server
  PolySearch performs multiple types of genome-wide searches, with a special (but not exclusive) emphasis on human disease. It also supports PubMed Literature searches on disease genes as well as gene name searches, SNP searches, mutation searches and PCR-primer searches.
• RCI
  RCI is a Python program that predicts protein flexibility by calculating the Random Coil Index from backbone chemical shifts (CA, CO, CB, N, HA) and estimating values of model-free order parameters as well as per-residue RMSD of NMR and MD ensembles from the Random Coil Index. Download Alternative Mirror
• PREDITOR
  PREDITOR is a program for PREDIcting φ, ψ, χ₁, and ω TORsion angles in proteins  from ¹³C, ¹⁵N and ¹H chemical shifts and sequential homology. PREDITOR 30^o-accuracy of predicting φ and ψ is close to 90%. The average χ₁ accuracy is 84% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification. Overall, the program is 35X faster and its predictions are approximately 20% better than existing methods.
• SimCell
  SimCell is a DCA Cell simulator used to simulate cellular and biochemical processes.The user, through the use of the SimCell Interface may create: small molecules, membrane, membrane proteins, protein/RNA molecules, DNA molecules and Genes. These cellular components can then interact amongst themselves to create fascinating new processes.
• PANAV
  PANAV is a Java based structure-independent chemical shift validation and re-referencing tool. It is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. Download

Research Staff and Students

Lab Presentation Slides

• Click here to visit our lab presentations page

Programs (Source and Binary)

• JVIEW
  A user friendly program for calculating coupling constants from TOCSY, NOESY, HMQC traces.
• PHIPSI2CS
  A program for calculating chemical shifts from polypeptide phi, psi backbone dihedral angles.
• SHIFTY
  A program for predicting protein chemical shifts using only sequence information.
• SEQSEE
  A complete program suite for protein sequence analysis. Runs on UNIX platforms.
• VADAR
  A program for evaluating protein structures (Volume Area Dihedral Angle Reporter). Runs on UNIX platforms.
• XALIGN
  A program for aligning multiple protein sequences that uses secondary structure information in the alignment process. Runs on UNIX platforms.
• XREF
  This is a script based on Varian's MAGICAL language. The macro is useful for referencing heteronuclear experiments where no reference signal from an observable internal standard is available. This macro will reference `<sup>1</sup>H', `¹³C', `<sup>15</sup>N', `¹⁹F' and `<sup>31</sup>P' nuclei up to four dimensions. Please refere to `xref' manual for more information. The current version of this macro is V2.0 which updated on February 9th, 2001 at this server.
• PANAV
  A Java based structure-independent chemical shift validation and re-referencing tool. It is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. 
• Our Download Page
  

Places

• University of Alberta
  
• Department of Biological Science, U of A
  
• Department of Computing Science, U of A
  
• Department of Computing Science,Graduate Programs and Admissions
  
• Department of Biological Science,Graduate Studies Program
  
• Biotools Incorporated
  
• Chenomx Incorporated
  
• BRONCO home page
  
• PENCE Homepage
  
• PENCEBioinformatics Group
  
• BioMagResBank
  
• Protein Data Bank
  
• Some Neat Animation
  

Pictures

• Directions to the lab
  
• HAV 3C Protease
  
• T4 Thioredoxin
  
• Peptide Micelle
  

Protocols

• Poster printing instructions.AICT (formerly CNS)
• PowerPoint for XP
  
• Creation of high resolution images (300 dpi or greater) by Paul Stothard
  
• SVN Versioning by Joseph Cruz
  

Courses

• Bioinfo 301 - Introduction to Bionformatics
  
• Bioinfo 401 - Advanced topics in bioinformatics
  
• Micro 343 - Topics in Microbial Laboratory Techniques
  
• Pharm 321 - Protein Pharmaceuticals
  
• Pharm 325 - Introduction to Quantitative Pharmaceutical Analysis
  
• Pharm 341 - Pharmaceutical Technology I
  
• Pharm 360 - Protein Pharmaceutics
  
• Pharm 361 - Protein Formulation & Delivery
  
• Pharm 493 - Pharmaceutical Biotechnology
  
• Pharm 580 - Introduction to Computer-Aided Drug Design
  
• Pharm 610 - Advanced Physical Pharmacy
  
• Pharm 570 - Advanced Pharmaceutical Analysis - Spectroscopy
  

Woods Hole Conference 2005

Book Figures

pharmacy, University of Alberta, Pharmaceutical Sciences, shifty, proteins, peptides, Wishart, Chemical, Shifts, Chemical Shift Prediction, Bioinformatics, Computer aided Drug Design, NMR, NMR Spectroscopy, Protein Engineering, Micelles, Peptide synthesis, Antibody Engineering, Protease, Wishart Pharmaceutical Research Group - Protein Engineering, Chemical Shift Prediction, NMR Spectroscopy, Peptide Synthesis, and Antibody Engineering at the University of Alberta