Mitsu Ikura Lab

Connecting protein structures to signaling biology

Useful Sites

Databases | Genomes | Protein Structure Tools | NMR| Crystallography | Green Fluorescent Protein | Calcium binding proteins | Invitrogen | Enzymology | Search engines | Dictionaries/Encyclopaedias | Journals | Software | Financial support | UHN Message Board | U of T / UHN Community |

Databases
- The Protein Data Bank
- EBI Macromolecular Structure Database
- BioMagResBank
- SWISS-PROT
- NCBI
- TIGR
- Nucleic Acids Research Molecular Biology Database List
Genomes
- Prokaryotes
- Archaebacteria
- Eukaryotes
- Other links
Protein Structure Tools
- ClustalW at PBIL
- Database of Macromolecular Movements
- European Molecular Biology Laboratory (EMBL) services
- EBI links
  - Fasta - search for protein sequences
  - Blast - search for protein sequences
  - ClustalW - multiple sequence alignment
  - PRATT - pattern searching in non-aligned sequences
  - Dali/FSSP - fold classification based on protein structure-structure alignment
- MODELLER - homology protein structure modelling
- SCOP - structural classification of proteins
- THREADER - protein tertiary structure prediction
- University College London Biochemistry Biocomputing Group (Prof. Christine Orengo's site)
  - CATH - protein structural classification
  - CATHserver
  - PROCHECK - check the stereochemical quality of a protein structure
  - Protein-protein Interaction Server - calculate interacting surface areas between molecules
- University College London Bioinformatics Unit (Prof. David Jones' site)
  - PSIPRED
  - GenTHREADER
  - THREADER
  - MEMSAT
  - GTD
  - DomPred
  - DISOPRED
  - BioRAT
  - COPS
  - GeneWeaver
NMR
- Tools
- Research Groups
Crystallography
- Crystallographic tool information page
- Synchrotron radiation sources
Green Fluorescent Protein (GFP)
- GFP/Universal Imaging page
- GFP Newsgroup Archive
Calcium Binding Proteins
- EF-hand CaBP Data Library at Vanderbilt
- Walter Chazin Group
- PENCE
- Torbjorn Drakenberg Group
Invitrogen: Pichia pastoris Expression
- Manuals
- Frequently used manuals:
  - Pichia EasySelect System
  - Direct PCR
  - Pichia Multicopy System
  - Pichia Expression System
Enzymology
- Kinetics and ligand-binding resources
Search
- PubMed literature search
- Yahoo! Science - Biology - Structural Biology
- Pedro's Biomolecular Research Tools
- Links to Bioinformatics Resources (Department of Genetics, Hospital for Sick Children)
Dictionaries and Encyclopaedias
- Encyclopaedia Britannica
- Webster's Dictionary
- On-line Medical Dictionary
- Life Science Dictionary
- Cell Biology Topics
Journals
- BioMed Central Journals
- Biochemistry
- Biochem. J
- Cell
- Current Biology
- EMBO Journal
- European Journal of Biochemistry
- Journal of the American Chemical Society
- Journal of Biological Chemistry
- Journal of Biomolecular NMR
- Journal of Molecular Biology
- Journal of Functional and Structural Genomics
- Molecular Cell
- Nature
- Nature Biotechnology
- Nature Review Molecular and Cell Biology
- Nature Structural Biology
- Proceedings of the National Academy of Sciences
- Proteins: Structure, Function and Genetics
- Protein Science
- Science
- Structure
- Trends in Biochemical Sciences
Software
- PyMol
- CNS
- GRASP
- InsightII
- MOLMOL
- MolScript
- NMRView
- RasMol
- Raster3D
- X-PLOR
Financial support for our research
- Canadian Foundation for Innovation
- Cancer Research Society
- Howard Hughes Medical Institute International Research Scholars Program
- Canadian Institutes of Health Research
- (formerly Medical Research Council of Canada)
- National Cancer Institute of Canada
- CIHR Membrane Protein Training Site
- Heart and Stroke Foundation of Canada
U of T / UHN Community
- Princess Margaret Hospital
- Univeristy Health Network
- University of Toronto
- Medical Biophysics U of T
- T-Space Production Server

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