[转载]代谢和信号途径

6. Metabolic Enzymes and Pathways; Signaling Pathways
Pathguide	A listing of pathway, signal transduction and protein-protein interaction databases		http://pathguide.org
6.1. Enzymes and enzyme nomenclature
BRENDA	Enzyme names and biochemical properties		http://www.brenda-enzymes.info/
ENZYME	Enzyme nomenclature and properties		http://www.expasy.org/enzyme/
Enzyme Nomenclature	IUBMB Nomenclature Committee recommendations		http://www.chem.qmul.ac.uk/iubmb/enzyme/
EzCatDB	Enzyme Catalytic Mechanism Database		http://mbs.cbrc.jp/EzCatDB/
FCP	Functional coverage of the proteome by structures		http://cgl.imim.es/fcp/
IntEnz	Integrated enzyme database and enzyme nomenclature		http://www.ebi.ac.uk/intenz
MACiE	Mechanism, annotation and classification in enzymes: enzyme reaction mechanisms		http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
ORENZA	ORphan ENZymes database		http://www.orenza.u-psud.fr/
PRECISE	Predicted and Consensus Interaction Sites in Enzymes		http://precise.bu.edu/precisedb/
PROCOGNATE	Protein cognate ligands for the domains in enzyme structures		http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html
SCOPEC	Mapping of catalytic function to domain structure		http://www.sbinf.org/~richard/enzome/
TECRdb	Thermodynamics of enzyme-catalyzed reactions		http://xpdb.nist.gov/enzyme_thermodynamics
6.2. Metabolic pathways
BioCarta	Online maps of metabolic and signaling pathways		http://www.biocarta.com/genes/allPathways.asp
BioCyc	Pathway/genome databases for many bacteria		http://biocyc.org/
Biodegradative Strain Database	Microorganisms that can degrade aromatic and other organic compounds		http://bsdNaNe.msu.edu/
BioSilico	Integrated access to various metabolic databases		http://biosilico.kaist.ac.kr
HMDB	The Human Metabolome Database: Curated human metabolite and metabolism data		http://www.hmdb.ca
KEGG Pathway	Metabolic and regulatory pathways in complete genomes		http://www.genome.jp/kegg/pathway.html
Lipid MAPS	Lipid metabolites and pathways strategy		http://www.lipidmaps.org
MetaCyc	Metabolic pathways and enzymes from various organisms		http://metacyc.org
PathDB	Biochemical pathways, compounds and metabolism		No longer maintained
Reactome	Database of metabolic and signaling pathways		http://www.reactome.org/
SYSTOMONAS	SYSTems biology of pseudOMONAS		http://www.systomonas.de/
UM-BBD	University of Minnesota biocatalysis and biodegradation database		http://umbbd.msi.umn.edu/
6.3. Protein-protein Interactions
3DID		3D interacting domains: Domain-domain interactions in proteins with known 3D structures	http://3did.embl.de/
3D-Interologs		Protein-protein interactions in various evolutionary lineages	http://gemdock.life.nctu.edu.tw/3D-Interologs
AffinDB		Affinity data for protein-ligand complexes	http://www.agklebe.de/affinity
aMAZE		A system for the annotation, management, and analysis of biochemical and signalling pathway networks	http://www.scmbb.ulb.ac.be/amaze/
AtPID		Arabidopsis thaliana Protein Interactome Database	http://atpid.biosino.org/
Bacteriome.org		Protein interaction database for E. coli	http://www.bacteriome.org
BIND		Biomolecular interaction network database	No longer free for all
Binding MOAD		Binding Mother of All Databases: protein-ligand crystal structures	http://www.BindingMOAD.org
BioGRID		Genetic and physical interactions in yeast, worm and fly	http://www.thebiogrid.org
BRITE		Biomolecular Relations in Information Transmission and Expression	http://www.genome.ad.jp/brite
CellCircuits		Molecular network models: from pairwise molecular interactions to whole pathways	http://www.cellcircuits.org
CORUM		Experimentally verified mammalian protein complexes	http://mips.gsf.de/genre/proj/corum
CutDB		Community annotation resource for proteases, their substrates and cleavage sites	http://cutdb.burnham.org/
DDIB		Database of domain interactions and binding	http://www.ddib.org/
DIMA		Domain interaction map: experimental data and predictions on protein domain interactions	http://mips.gsf.de/genre/proj/dima2
DIP		Database of interacting proteins: Experimentally-determined protein-protein interactions	http://dip.doe-mbi.ucla.edu
Dockground		Protein-protein interfaces in co-crystallized protein structures	http://dockground.bioinformatics.ku.edu/
DOMINE		Known and predicted protein domain interactions in PDB entries	http://domine.utdallas.edu
DOMINO		Domain peptide interactions	http://mint.bio.uniroma2.it/domino/
DRC		Database of ribosomal crosslinks	http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
HotSprint		Hot spots (functionally and structurally important residues) in protein interfaces	http://prism.ccbb.ku.edu.tr/hotsprint/
hp-DPI		Database of protein interactions in Helicobacter pylori	http://dpi.nhri.org.tw/hp/
HPID		Human protein interaction database	http://www.hpid.org
I2D		Interologous Interaction Database: Predicted protein-protein interactions in humans	http://ophid.utoronto.ca/i2d
IntAct		Protein-protein interaction data	http://www.ebi.ac.uk/intact/
Inter-Chain Beta-Sheets		Protein interactions mediated by interchain beta-sheet formation	http://www.igb.uci.edu/servers/icbs/
InterDom		Putative protein domain interactions	http://interdom.i2r.a-star.edu.sg/
KDBI		Kinetic data of bio-molecular interactions	http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php
LigAsite		Biologically relevant binding sites in proteins with known structures	http://www.scmbb.ulb.ac.be/Users/benoit/LigASite
MiMI		Michigan Molecular Interactions: Protein-protein interactions	http://mimi.ncibi.org/MiMI/home.jsp
MINT		Molecular INTeraction	http://mint.bio.uniroma2.it/mint/
OPHID		Online predicted human interaction database	Superseded by I2D (no. 897)
PDZBase		Protein-protein interactions involving PDZ domains	http://icb.med.cornell.edu/services/pdz/start
PepCyber:P~Pep		Human protein interactions mediated by phosphoprotein-binding domains	http://PepCyber.umn.edu/PepCyber
PINdb		Proteins interacting in nucleus (human and yeast)	http://pin.mskcc.org
POINT		Prediction of human protein-protein interactome	http://point.bioinformatics.tw
ProNIT		Protein-nucleic acid interactions	http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
PROTCOM		3D structures of two-chain protein complexes	http://www.ces.clemson.edu/compbio/protcom
PSIbase		Interaction of proteins with known 3D structures	http://psimap.org/index.php/PSIMAP
SNAPPI		Structures, iNterfaces and Alignments for Protein-Protein Interactions	http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp
STITCH		Search Tool for Interactions of Chemicals	http://stitch.embl.de
Structurally conserved interfaces		Interacting residues in protein-protein interfaces in PDB	http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
The Cell Cycle DB		Genes and proteins involved in human and yeast cell cycle	http://www.itb.cnr.it/cellcycle
UniHI		Unified Human Interactome: human protein-protein interactions	http://www.mdc-berlin.de/unihi
6.4. Signaling pathways
BioCarta		Online maps of metabolic and signaling pathways	http://www.biocarta.com/genes/allPathways.asp
Cyclonet		Database on cell cycle regulation	http://cyclonet.biouml.org/index.html
EndoNet		Information on endocrine networks	http://endonet.bioinf.med.uni-goettingen.de/
Hedgehog signalling		Resources and annotations of the Hedgehog signaling pathway	http://hedgehog.sfsu.edu/
NetworKIN		Network approach to human protein kinases and their substrates	http://networkin.info/
PhosPhAt		Arabidopsis Protein Phosphorylation Site Database	http://www.plantenergy.uwa.edu.au/applications/phosphat/index.html
PRRDB		Pattern recognition receptors and their ligands	http://www.imtech.res.in/raghava/prrdb/
pSTIING		Protein signalling, transcriptional interactions and inflammation networks gateway	http://pstiing.licr.org/
ROSPath		Reactive oxygen species (ROS) signaling pathway	http://rospath.ewha.ac.kr
STCDB		Signal Transduction Classification Database	http://bibiserv.techfak.uni-bielefeld.de/stcdb/
UCSD-Nature Signaling Gateway		Expert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling	http://www.signaling-gateway.org/molecule/

 

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