42 CATALYZING INQUIRY
TABLE 3.1 Continued
Category Databases and URLs
Gene expression: Unigene: http://www.ncbi.nlm.nih.gov/UniGene/
microarray and cDNA
gene expression dbEST (Expression Sequence Tag Database):
http://www.ncbi.nlm.nih.gov/dbEST/index.html
BodyMap: http://bodymap.ims.u-tokyo.ac.jp/GEO (Gene Expression Omnibus): http://www.ncbi.nlm.nih.gov/geo/Structure: three- PDB (Protein Data Bank): http://www.rcsb.org/pdb/index.html
dimensional structures of
small molecules, proteins, NDB (Nucleic Acid Database):
nucleic acids (both RNA http://ndbserver.irutgers.edu/NDB/ndb.html
and DNA) folding
predictions CSD (Cambridge Structural Database):
http://www.ccdc. cam. ac.uk/prods/csd/csd.html
Classification of protein SCOP (Structure Classification of Proteins):
family and protein http://scop.mrc-Imb.cam.ac.uk/scop/
domains
CATH (Protein Structure Classification Database):
http://www.biochem.ucl.ac.uk/bsm/cath-new/index.html
Pfam: http://pfam.wustl.edu/PROSITE database for protein family and domains:
http://www.expasy.ch/prosite/BLOCK: http://www.blocks.fhcrc.org/Protein pathway KEGG (Kyoto Encyclopedia of Genes and Genomes):
Protein-protein http://www.genome.ad.jp/kegg/kegg2.html#pathway
interactions and
metabolic pathway BIND (Biomolecular Interaction Network Database):
http://www.binddb.org/
DIP (Database of Interacting Proteins): http: Hdip.doe-mbi.ucla.edu/EcoCyc (Encyclopedia of Escherichia coli Genes and Metabolism):
http://ecocyc.org/ecocyc/ecocyc.htmlWIT (Metabolic Pathway): http://Hwit.mcs.anl.gov/WIT2/Proteomics: proteins, AFCS (Alliance for Cellular Signaling): http://cellularsignaling.org/
protein family
JCSG (Joint Center for Structure Genomics):
http://www.jcsg.org/scripts/prod/home.html
PKR (Protein Kinase Resource): http://pkr.sdsc.edu/html/index.shtml