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Home > Extras > Bioinformatics For Dummies® Bonus Material
Bioinformatics For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.
 

[Bio FD Home][Ch.1][Ch.2][Ch.3][Ch.4][Ch.5][Ch.6][Ch.7][Ch.8][Ch.9][Ch.10][Ch.11][Ch.12][Ch.13][Ch.15]

Chapter 4: Using Protein and Specialized Sequence Databases

Chapter 4 images

The two main information resources about protein sequences

Address Description
www.expasy.org/sprot/ The Expasy/SWISS-PROT server
pir.georgetown.edu The Protein Information Resource server

Some good places for refreshing your biochemistry

Address Description
www.glycosuite.com The glycan structure database
lipid.bio.m.u-tokyo.ac.jp The ultimate lipid database
chem.sis.nlm.nih.gov/chemidplus/ ChemIDplus: Identifying molecules by drawing them up!

The main resources for biochemical pathways and enzymes

Address Description
www.expasy.ch/cgi-bin/search-biochem-index Find which metabolic pathway a molecule belongs to.
www.genome.ad.jp/kegg/ The famous Kyoto Encyclopedia of Genes and Genomes (KEGG). E.C. (Enzyme Codes) numbers or gene names are the best starting points for this resource.
brenda.bc.uni-koeln.de

The comprehensive enzyme information system BRENDA.
www.chem.qmul.ac.uk/iubmb The official site for enzyme nomenclature of the International Union of Biochemistry and Molecular Biology (IUBMB).
www.ecocyc.org The Encyclopedia of E. coli Genes and Metabolism. It is progressively extending to other bacteria.

Some great 3-D structure information resources

Address Description
www.rcsb.org/pdb PDB, the official repository database for protein 3-D structures.
www.ncbi.nlm.nih.gov/Structure MMDB, NCBI's database of macromolecular 3-D structures with visualization tools.
scop.mrc-lmb.cam.ac.uk/scop

SCOP, a Structural Classification Of Proteins.
www.biochem.ucl.ac.uk/bsm/cath_new CATH (Class, Architecture, Topology, Homologous superfamily), a hierarchical classification of protein structures.
www.expasy.ch/swissmod/SWISS-MODEL.html Swiss-Model, a fully automated protein structure homology-modeling server.

Some specialized protein databases

Address Description
imgt.cines.fr IMGT, the International Immunogenetics database, specializes in proteins involved in the immune response.
rebase.neb.com Rebase, the reference restriction-modification enzyme database.
afmb.cnrs-mrs.fr/CAZY

CAZy, an information resource on enzymes that degrade, modify, or create glycosidic bonds.
www.merops.co.uk MEROPS, a database specializing on proteases.
pkr.sdsc.edu/html/index.shtml PKR, the Protein Kinase Resource, focuses on the protein kinase family of enzymes.
nrr.georgetown.edu NRR, the Nuclear Receptor Resource, is a collection of individual databases on the steroid and thyroid hormone receptors.
senselab.med.yale.edu/senselab The Human Brain Database provides information on the proteins involved in neural processes, such as ion channels, membrane receptors of neurotransmitters and neuromodulators, as well as olfactory receptors (ORDB).
www.ncbi.nlm.nih.gov/COG The COG (Cluster of Orthologous Groups) database regroups proteins shared by at least three major phylogenetic lineages (ancient conserved domains).

 
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