Faculty of Biological Sciences
Useful Links
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Miscellaneous
- FindAPhD.com
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- Magnetosome meeting reports
Meetings
- UK/South East USA symposium on Structural Genomics and Proteomics of Membrane- and Metallo-Proteins
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 Letters
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- Molecular Membrane Biology
- Nature
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- Science
- Trends in Biochemical Sciences
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- Trends in Endocrinology and Metabolism
University of Leeds
- Bodington Common
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- Radioactive Source Database Login
Teaching resources
- Molecular Cell Biology (Lodish et al.)
- Biochemistry in 3D-Lehninger Principles of Biochemistry
- Histology Website
Funding agencies
- RPA Forms
- BBSRC
- Je-S 1 (Joint electronic submission system)
- MRC
- MRC eaa (electronic applications login)
- The Wellcome Trust
- Royal Society
- Leverhulme
Genome databases
- The I.M.A.G.E. consortium
- TIGR (The Institute for Genome Research, part of the J. Craig Venter Institute)
- DiArk
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)
Yeast
- SGD (Saccharomyces Genome Database)
- Candida DB
- Candida homepage (Stanford Genome Technology Center)
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)
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)
Others
- BDGP (The Berkeley Drosophila Genome Project)
- Ciona intestinalis genome database
- TAIR (The Arabidopsis Information Resource)
- Aspergillis nidulans Database
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)
Protein sequence databases
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
Other Information
- BioWurld (a semi-automated index of resources in the fields of bioinformatics and molecular biology)
- 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
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
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
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)
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
Database Searching and Sequence Alignment
- BLAST searches at NCBI
- Clustalw2 Multiple sequence alignment
- MUSCLE Multiple sequence alignment
- PROBCONS Multiple sequence alignment
- Fasta3 sequence similarity searches at EBI
- PHYLIP home page
- TreeView
Techniques
Commercial companies and other sources of materials
Antibodies
- Abcam Ltd.
- The Antibody Resource Page
- LifeSpan BioSciences
- Serotec
- Stressgen Bioreagents
- Developmental Studies Hybridoma Bank
Radiochemicals
- Amersham Radiochemicals (GE Healthcare)
- International Isotopes Clearing House, Inc.
- Moravek Biochemicals
- OlChemIm Ltd
- Perkin Elmer Life Sciences (NEN)
- Ambion
- Avidity
- Clontech
- Geneservice Ltd (IMAGE clones)
- Invitrogen: Life Technologies
- MP Biomedicals
- New England Biolabs
- Novagen
- OriGene
- Promega
- Qiagen
- Stratagene
Cells and DNA
- ATCC (American Type Culture Collection)
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