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.

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.
• SHIFTX2 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 for both backbone and sidechain atoms.
• SHIFTY Web Server
  A web server for predicting protein chemical shifts using only amino acid sequence information.
• 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.
• 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
• PANAMP Sample Automation
  PANAMP Sample Automation is a java-enabled, web-based automation tool, designed to process a batch of samples, given a calibration text file, a library text file, and a data folder containing the text files of GcMS runs of the samples.

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
  
• Chenomx Incorporated
  
• BRONCO home page
  
• 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
  

Book Figures