Useful Links

Jump to:

Search engines Miscellaneous Meetings Journals University of Leeds Teaching resources

Funding agencies Genome databases Protein sequence databases Plant Resources Protein sequence databases Membrane biology

Other information Structure databases DNA and protein analysis tools Techniques Commercial companies and other sources of materials

---

Search engines

• Google
• Yahoo

top of list

Miscellaneous

• FindAPhD.com
• Google Maps
• Multimap
• Northenden Travel Group
• National Rail Enquiries
• Guardian Unlimited Film
• UK Universities Map
• MPSI
• Leeds PIMS
• Diamond Log-on
• Magnetosome meeting reports

top of list

Meetings

• UK/South East USA symposium   on Structural Genomics and Proteomics of Membrane- and Metallo-Proteins

top of list

Journals

• Entrez PubMed   (Retrieval of references from the PubMed database using the NCBI Entrez retrieval system)
• PubCrawler   (an Update Alerting Service for PubMed and GenBank)
• Web of Knowledge   (ISI Web of Science®)
• Leeds University Library   (Electronic Resources)

• American Journal of Physiology
• Biochemical Journal
• Biochemistry
• BioTechniques
• Cell
• EMBO Journal
• FEBS Journal
• FEBS Letters
• Journal of Biological Chemistry
• Journal of Cell Science
• Journal of Cell Biology
• Molecular and Cellular Biology
• Molecular Membrane Biology
• Molecular Microbiology
• Nature
• Nature Biotechnology
• Nature Cell Biology
• Nature Genetics
• Nature Medicine
• Nature Reviews - Molecular Cell Biology
• Nature Structural and Molecular Biology
• Proc. Natl. Acad. Sci. USA
• Science
• Traffic
• Trends in Biochemical Sciences
• Trends in Cell Biology
• Trends in Endocrinology and Metabolism

top of list

University of Leeds

• University of Leeds

• Bodington Common
• Faculty of Biological Sciences
• Faculty of Biological Sciences - Seminars
• Library
• Media Services
• Research Support Unit
• Student and staff email lookup
• University of Leeds Calendar
• Faculty Research Support Office
• Symplectic Publications Management System
• Room Bookings
• Redeployment register
• Radioactive Source Database Login

top of list

Teaching resources

• Molecular Cell Biology (Lodish et al.)
• Biochemistry in 3D-Lehninger Principles of Biochemistry
• Histology Website

top of list

Funding agencies

• RPA Forms
• BBSRC
• Je-S 1 (Joint electronic submission system)
• MRC
• MRC eaa (electronic applications login)
• The Wellcome Trust
• Royal Society
• Leverhulme
• Research Fortnight Online

top of list

Genome databases

• The I.M.A.G.E. consortium
• TIGR   (The Institute for Genome Research, part of the J. Craig Venter Institute)
• DiArk

top of list

Nematodes

• BaNG (Blaxter Lab Nematode Genomics)
• The C. elegans Gene Knockout Consortium
• Filarial Genome Network
• Sanger Centre   (The C. elegans Genome Project)
• SGD Worm-Yeast Protein Comparison
• WormBase   (Caenorhabditis elegans)
• WWW Server   (Caenorhabditis elegans)

top of list

Yeast

• SGD  (Saccharomyces Genome Database)
• Candida DB
• Candida homepage  (Stanford Genome Technology Center)

top of list

Bacteria

• CyberCell Database  (Escherichia coli)
• Colibri  (Escherichia coli)
• TubercuList  (Mycobacterium tuberculosis)
• SubtiList  (Bacillus subtilis)
• PyloriGene  (Helicobacter pylori)
• MypuList  (Mycobacterium pulmonis)
• Leproma  (Mycobacterium leprae)
• Listilist  (Listeria)

top of list

Protozoa

• Leishmania Genome Network
• Malaria Genetics & Genomics (NCBI)
• Parasite Genome Website (EBI)
• PlasmoDB (The Plasmodium Genome Resource)
• Plasmodium falciparum Genome Project (Sanger Centre)
• WU-Blast2 Server (EBI) (Parasite Genomes)

top of list

Others

• BDGP  (The Berkeley Drosophila Genome Project)
• Ciona intestinalis genome database
• TAIR  (The Arabidopsis Information Resource)
• Aspergillis nidulans Database

top of list

Plant Resources

• Signal T-DNA Express
• Aramemnon (Plant membrane protein database)
• TAIR (The Arabidopsis Information Resource)
• NASC (The European Arabidopsis Stock Centre)
• ABRC (Arabidopsis Biological Resource Centre)
• RARGE (RIKEN Arabidopsis & Genome Encyclopedia)
• Arabidopsis GFP database (John Innes Centre)
• Plant Cell Imaging (Carnegie Institution)
• Genevestigator
• ACT (Arabidopsis Coexpression Data Mining Tools)

top of list

Protein sequence databases

• InterPro
• Pfam
• PROSITE
• SMART
• UniProt

top of list

Membrane biology

• Arabidopsis Membrane Protein Library
• PlantsT Functional genomics of plant transporters
• The E. coli Cell Envelope Protein Data Collection
• TransportDB (Genomic comparisons of membrane transport systems)
• Membrane proteins of known structure
• Transport protein database
• Yeast Membrane Protein Library
• Yeast Transport Protein Database
• MPDB Membrane Protein Databank
• JCIMPT Joint Center for Innovative Membrane Protein Technologies
• SLC Transporter Gene Tables

top of list

Other Information

• Apoptosis online

• BioWurld (a semi-automated index of resources in the fields of bioinformatics and molecular biology)

• GFP-cDNA Localisation Project

• iHOP Information Hyperlinked over Proteins

Statistics

• What test do I need? Statistical tests for significance
• Statistics at Square One The t tests (from BMJ Publishing Group Ltd)
• Grubb's test for outliers

top of list

Structure databases

• PDB (Protein Data Bank)
• Chemicals with Pharmaceutical Activity (3D Structure Database)
• Chime Resources at UMass
• HIC-Up (Hetero-compound Information Centre - Uppsala)
• Klotho: Biochemical Compounds Declarative Database
• small molecules (Library of 3-D molecular structures)
• 3-D Virtual Chemistry Library

top of list

DNA and protein analysis tools

DNA Analysis

General

• The Sequence Manipulation Suite (Programs for analyzing and formatting DNA and protein sequences, including determination of similarities and identities from alignments)
• The European Bioinformatics Institute (EBI) toolbox bioinformatic tools including sequence format conversion
• Codon usage tables
• JCat On-line codon adaptation tool
• EMBOSS Transeq (Translation machine)
• JaMBW 1.1 Java based Molecular Biologist's Workbench (for reverse, complement, inverse)
• LITBIO Laboratory for Interdisciplinary Technologies in Bioinformatics
• MBS - Molecular Biology Shortcuts
• NEBcutter Restriction mapping
• Translate tool (Expasy) (Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.)
• GENE INFINITY
• The Bio-Web

Primer design

• PrimerX (Design of primers for site-directed mutagenesis)
• OligoAnalyzer Primer design

top of list

Protein Analysis

General

• ExPASy Proteomics tools
• TarO Target Optimisation Utility
• OPAL Protein Analysis Linker

Disorder prediction

• Fold Index Protein Disorder Prediction
• RONN Protein Disorder Prediction
• DisEMBL Protein Disorder Prediction
• DISOPRED2 Protein Disorder Prediction
• DRIP-PRED Protein Disorder Prediction
• DomPred Protein Domain Prediction

Secondary structure prediction

• Coils Prediction of coiled coil regions in proteins (Lupas's method) at EMBnet-CH
• Paircoil2 Prediction of coiled coil regions in proteins (Berger's method)
• Multicoil
• PSIPRED Protein Structure Prediction Server
• DSSP Definition of protein secondary structure

Membrane topology prediction

• Phobius  A combined transmembrane topology and signal peptide predictor
• Membrane Protein Explorer
• TMHMM (v. 2.0)  Prediction of transmembrane helices in proteins (CBS; Denmark)
• HMMTOP  Prediction of transmembrane helices in proteins (Institute of enzymology, Budapest)
• The PredictProtein server Prediction of transmembrane helix location and topology (Columbia University)
• TMAP Transmembrane detection based on multiple sequence alignment (Karolinska Institut; Sweden)
• TM-Finder Prediction of transmembrane helices
• TOP-MOD
• TOPCONS Consensus prediction of protein topology

Threading and homology modelling

• The ConSeq Server surface-mappingof phylogenetic information for the identification of functional regions in proteins
• LOOPP Protein Structure Prediction Server
• MMM Server Sequence-to-Structure alignment
• MolProbity structure validation for proteins and nucleic acids
• CMA:Contact Map Analysis
  

top of list

Database Searching and Sequence Alignment

• BLAST searches at NCBI
• Clustalw2 Multiple sequence alignment
• TCoffee Multiple sequence alignment
• MUSCLE Multiple sequence alignment
• PROBCONS Multiple sequence alignment
• Fasta3 sequence similarity searches at EBI
• PHYLIP home page
• TreeView

top of list

Techniques

• Baculovirus.com
• BSGC Protocols and Methods
• Tagged protein purification

top of list

Commercial companies and other sources of materials

Antibodies

• Abcam Ltd.
• The Antibody Resource Page
• LifeSpan BioSciences
• Serotec
• Stressgen Bioreagents
• Developmental Studies Hybridoma Bank

top of list

Radiochemicals

• Amersham Radiochemicals (GE Healthcare)
• International Isotopes Clearing House, Inc.
• Moravek Biochemicals
• OlChemIm Ltd
• Perkin Elmer Life Sciences (NEN)

top of list

• Ambion
• Avidity
• Clontech
• Geneservice Ltd (IMAGE clones)
• Invitrogen: Life Technologies
• MP Biomedicals
• New England Biolabs
• Novagen
• OriGene
• Promega
• Qiagen
• Stratagene

top of list

Cells and DNA

• ATCC  (American Type Culture Collection)

top of list

Miscellaneous Sources of Materials

• Anatrace
• Avanti Polar Lipids
• Bio-Rad
• Cell Signaling Technology  (NEB company)
• IBA GmbH
• InforMax Inc.
• Improvision
• Merck Biosciences Ltd.  (Calbiochem; Novabiochem; Novagen; Oncogene Research Products)
• Molecular Dimensions Ltd
• Molecular Probes
• P-CUBE
• Pierce Chemical
• Stratech Scientific Ltd
• TCS Biosciences Ltd
• Science Warehouse

top of list