John Mitchell Group

Protein/Ligand databases online

The table below provides a list of some of the current protein & protein / ligand databases available.

Database Name

Content

World Wide Web Address
MACiE
Enzyme reaction mechanisms
http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
EzCatDB
Enzymes
http://mbs.cbrc.jp/EzCatDB/
SFLD
Enzyme structure & function
http://sfld.rbvi.ucsf.edu/
PLD
Protein ligand interaction data
http://chemistry.st-andrews.ac.uk/staff/jbom/group/PLD.xls
PDB
Protein structural data
http://www.rcsb.org/pdb/Welcome.do
CSD
Molecule structural data
 http://www.ccdc.cam.ac.uk/
PDBSum
Summarises PDB files
 http://www.biochem.ucl.ac.uk/bsm/pdbsum/index.html
CATH
Classification of protein structural domains
 http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
SCOP
Structural classification of proteins
http://scop.mrc-lmb.cam.ac.uk/scop/
SWISS-PROT & Tr-EMBL
Protein sequence database
http://www.expasy.ch/sprot/sprot-top.html
GenBank
Genetic sequence database
http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html
Pfam
Protein domains
 http://www.sanger.ac.uk/Software/Pfam/
HSSP
Homology derived protein structures
 http://www.sander.ebi.ac.uk/hssp/
BLOCKS
Protein domains
 http:/blocks.fhcrc.org/
PRINTS
Protein fingerprints (group of conserved motifs indicative of protein family)
 http://bioinf.man.ac.uk/dbbrowser/PRINTS/
PIR
Protein sequence
 http://pir.georgetown.edu/
KEGG
Metabolic pathway
 http://www.genome.ad.jp/kegg/kegg2.html
LIGAND
Chemical compounds and reactions in biological pathways database
 http://www.genome.ad.jp/ligand/
CSNDB
Human signalling pathways database
http://www.chem.ac.ru/Chemistry/Databases/CSNDB.en.html
DIP
Protein interaction database
 http://dip.doe-mbi.ucla.edu/
BIND
Biological interaction database
http://www.bind.ca/
GRID
General Repository for Interaction Datasets
http://biodata.mshri.on.ca/grid
Binding Database
Measured binding affinities of biomolecules and synthetic compounds
http://www.bindingdb.org/bind/index.jsp