693
A selection of World Wide Web sites relevant to papers
published in this issue of Current Opinion in Structural Biology.
Addresses
*School of Cell and Molecular Biosciences, University of Newcastle
upon Tyne, Newcastle upon Tyne NE2 4HH, UK;
e-mail: d.a.chalton@ncl.ac.uk
†
San Diego Supercomputing Center, University of California
San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA;
e-mail: breddy@sdsc.edu
‡
Crystallography Department, Birkbeck College, London WC1E 7HX, UK;
e-mail: ubcg09j@mail.cryst.bbk.ac.uk
Current Opinion in Structural Biology 2002, 12:693–694
Biochemical reactions and enzyme catalysis
http://www.biologie.uni-hamburg.de/b-online/e18/18.htm
A resource from the University of Hamburg, Faculty of Biology,
this is a chapter from an Internet hypertext botany book. The
book describes biochemical reactions in detail, covering redox
reactions, properties and energy contents of chemical bonds,
mechanisms of enzyme catalysis, inhibition and regulation of
enzyme activities, and allosteric enzymes. Some helpful basic
thermodynamic terms are also given.
LIGAND: Database of Chemical Compounds and Reactions
in Biological Pathways
http://www.genome.ad.jp/ligand/
LIGAND is a GenomeNet resource from the Bioinformatics
Center, Institute of Chemical Research, Kyoto University. It is a
composite database consisting of COMPOUND, a collection
of chemical compounds that are related to various cellular
processes; REACTION, a collection of reactions, mostly enzy-
matic reactions, involving those compounds; ENZYME, the
enzyme nomenclature from IUBMB and IUPAC.
KEGG regulatory and metabolic pathways
http://www.genome.ad.jp/kegg/regulation.html
http://www.genome.ad.jp/kegg/metabolism.html
The Kyoto Encyclopaedia of Genes and Genomes (KEGG) is
an effort to computerise current knowledge of molecular and
cellular biology in terms of information pathways that consist of
interacting molecules or genes and to provide links to the gene
catalogues produced by genome sequencing projects. Graphical
pathway maps, orthologue group tables and molecular
catalogues are given for metabolic and regulatory pathways.
Ligand binding databases
http://sgedg.weizmann.ac.il/ferafael/ligdb.html
These ligand binding databases were created by Rafael
Najmanovich at the Weizmann Institute, Israel. The analysis was
restricted to ligands listed as HETATM in the PDB and excludes
nucleic acids, peptides and ligands that are covalently bound to
protein atoms, sulfates and phosphates. The three databases
are maximal database, binding pocket database and ligand
database. They are useful as a starting point for studies related
to ligand binding that require the structural comparison of apo
and holo forms of enzymes.
LGICdb: The Ligand-Gated Ion Channel Database
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
Ligand-gated ion channels are polymeric transmembrane proteins
involved in the fast response to numerous neurotransmitters.
There are three different superfamilies: the cys-loop superfamily,
ATP-gated channels and glutamate-activated cationic channels.
This database contains annotated nucleic acid and protein
sequence entries for ligand-gated ion channel subunits. It aims
to provide only one entry for each gene.
DIP: Database of Interacting Proteins
http://dip.doe-mbi.ucla.edu/
DIP
TM
is a database for the study of cellular networks of protein
interactions. It catalogues experimentally determined interac-
tions between proteins and combines information from a variety
of sources to create a single, consistent set of protein–protein
interactions. The data stored within the DIP database were
curated, both manually by expert curators and automatically
using computational approaches that use knowledge about
protein–protein interaction networks extracted from the most
reliable core subset of the DIP data.
BIND: Biomolecular Interaction Network Database
http://www.bind.ca/
BIND is a database designed to store full descriptions of inter-
actions, molecular complexes and pathways. The BIND data
model has virtually all components of molecular mechanisms,
including interactions between any two molecules composed of
proteins, nucleic acids and small molecules. Chemical reac-
tions, photochemical activation and conformational changes are
also described. Everything from small-molecule biochemistry to
signal transduction is abstracted in such a way that graph
theory methods may be applied for data mining. The database
can be used to study networks of interactions, to map pathways
across taxonomic branches and to generate information for
kinetic simulations.
MINT: a Molecular INTeractions database
http://cbm.bio.uniroma2.it/mint/
MINT is a database designed to store information about func-
tional interactions between biological molecules (proteins, RNA,
DNA). Beyond cataloguing the formation of binary complexes,
MINT was conceived to store details concerning the enzymatic
modification of one of the interacting partners. Presently, MINT
focuses on experimentally verified protein–protein interactions.
Both direct and indirect relationships are considered. MINT
consists of entries extracted from the scientific literature by
expert curators assisted by ‘MINT Assistant’, software that tar-
gets abstracts containing interaction information and presents
them to the curator in a user-friendly format. The interaction
Catalysis and regulation
Proteins
Web alert
David A Chalton*, Boojala Reddy
†
and Judith Murray-Rust
‡
Catalysis and regulation