Database Interactions

Network All (Pathways) Databases Exchange Formats Interaction Databases Metamining Databases Pathway Databases Predictive Interaction Databases Unifying Efforts Databases

Selecting node(s) shows a summary of database information below the network, with linkouts to database details from Pathguide, and to the database itself.

	The networks are adapted from: A graphical view of the world of protein-protein interaction databases, by Tomas Klingström and Dariusz Plewczynski. ICM, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Poland. The work was supported by Polish Ministry of Science and Higher Education N301 159735 grant.
	The networks are visualized with Cytoscape Web.

BIND - Biomolecular Interaction Network Database	. Protein-Protein Interactions . Genetic Interaction Networks	Details	Free	PSI-MI
BRITE - Biomolecular Relations in Information Transmission and Expression	. Protein-Protein Interactions	Details	Free
DIP - Database of Interacting Proteins	. Protein-Protein Interactions	Details		PSI-MI
LIGAND - Molecular building blocks of life in the chemical space	. Metabolic Pathways	Details	Free
aMAZE - Protein Function and Biochemical Pathways Project	. Protein-Protein Interactions . Metabolic Pathways . Transcription Factors / Gene Regulatory Networks	Details	Free
WIT - What Is There?	. Metabolic Pathways	Details
BioGRID - Biological General Repository for Interaction Datasets	. Protein-Protein Interactions . Genetic Interaction Networks	Details		PSI-MI
BioCyc - BioCyc Knowledge Library	. Metabolic Pathways	Details		BioPAX SBML
EcoCyc - Encyclopedia of E. coli Genes and Metabolism	. Metabolic Pathways	Details		BioPAX SBML
MetaCyc - Metabolic Pathway Database	. Metabolic Pathways	Details		BioPAX SBML
CSNDB - Cell Signaling Networks Database	. Signaling Pathways	Details
EMP - Enzymes and Metabolic Pathways Database	. Metabolic Pathways	Details	Free
ENZYME - Enzyme nomenclature database	. Metabolic Pathways	Details	Free
HPRD - Human Protein Reference Database	. Protein-Protein Interactions . Pathway Diagrams	Details		PSI-MI
JenPep - JenPep Peptide Binding database	. Protein-Protein Interactions	Details	Free
KEGG - Kyoto Encyclopedia of Genes and Genomes	. Metabolic Pathways . Pathway Diagrams	Details		BioPAX
MINT - Molecular Interaction Database	. Protein-Protein Interactions	Details	Free	PSI-MI
MIPS CYGD - MIPS Comprehensive Yeast Genome Database	. Protein-Protein Interactions . Metabolic Pathways . Pathway Diagrams . Genetic Interaction Networks	Details	Free	PSI-MI
NRR - Nuclear Receptor Resource	. Protein-Compound Interactions . Protein Sequence Focused	Details	Free
ooTFD - Object Oriented Transcription Factors Database	. Protein-Protein Interactions . Transcription Factors / Gene Regulatory Networks	Details
PathDB - Pathways Database	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways	Details
TRANSFAC - Transcription Factor Database	. Transcription Factors / Gene Regulatory Networks	Details
TRANSPATH - Signal Transduction Browser	. Signaling Pathways	Details
TRRD - Transcription Regulatory Regions Database	. Signaling Pathways . Transcription Factors / Gene Regulatory Networks	Details	Free
ABCdb - Archaea and Bacteria ABC transporter database	. Protein Sequence Focused	Details	Free
BioCarta - BioCarta Pathway Diagrams	. Pathway Diagrams	Details	Free
COMPEL - Database on Composite Regulatory Elements	. Transcription Factors / Gene Regulatory Networks	Details
DRC - Database of Ribosomal Crosslinks	. Protein-Protein Interactions	Details	Free
FIMM - Functional Molecular Immunology	. Protein-Protein Interactions	Details
GeneNet - Genetic Networks	. Metabolic Pathways . Signaling Pathways . Genetic Interaction Networks	Details	Free
GOLD.db - Genomics of Lipid-associated Disorders	. Metabolic Pathways . Signaling Pathways	Details	Free
Het-PDB_Navi - Het-PDB Navi	. Protein-Compound Interactions	Details	Free
ICBS - Inter-Chain Beta-Sheets	. Protein-Protein Interactions	Details	Free
KMIM - Kohn Molecular Interaction Maps	. Pathway Diagrams	Details	Free
MHCPEP - Database of MHC binding peptides	. Protein-Protein Interactions	Details
MPID-T - MHC-Peptide Interaction Database	. Protein-Protein Interactions	Details	Free
PATIKA - Pathway Analysis Tool for Integration and Knowledge Acquisition	. Metabolic Pathways . Signaling Pathways	Details
PDS - Pathways Database System	. Metabolic Pathways . Signaling Pathways	Details
PhosphoBase - Database of phosphorylation sites	. Protein-Protein Interactions . Protein Sequence Focused	Details
DroID - Drosophila Protein Interaction Map Database	. Protein-Protein Interactions . Genetic Interaction Networks	Details	Free
PubGene - PubGene	. Protein-Protein Interactions	Details	Free
RegulonDB - Database on Transcriptional Regulation and Genome Organization	. Transcription Factors / Gene Regulatory Networks	Details
SELEX_DB - Randomized DNA/RNA sequence database	Details	Free
SoyBase - USDA-ARS Soybean Genetics and Genome Database	. Metabolic Pathways	Details	Free
SYFPEITHI - Database of MHC Ligands and Peptide Motifs	. Protein-Protein Interactions	Details
UM-BBD - Biocatalysis/Biodegradation Database	. Metabolic Pathways	Details	Free
S/MARt_DB - The S/MAR transaction DataBase	. Protein-Protein Interactions	Details
SigPath - Signaling Pathway Information System	. Signaling Pathways	Details	Free
AARSDB - Aminoacyl-tRNA Synthetase Database	Details	Free
BindingDB - The Binding Database	. Protein-Compound Interactions	Details	Free
BRENDA - BRaunschweig ENzyme DAtabase	. Metabolic Pathways	Details
DBTBS - Database of Bacillus subtilis Promoters and Transcription Factors	. Transcription Factors / Gene Regulatory Networks	Details	Free
DPInteract - DNA-Protein Interactions Database	. Transcription Factors / Gene Regulatory Networks	Details	Free
GeNet - Gene Networks Database	. Transcription Factors / Gene Regulatory Networks	Details
HIVMID - HIV Molecular Immunology Database	. Protein-Protein Interactions	Details	Free
HoxPro - HOX Pro	. Transcription Factors / Gene Regulatory Networks	Details	Free
InBase - The Intein Database	. Protein Sequence Focused	Details	Free
Indigo - Gene Neighborhoods and Codon Usage	. Metabolic Pathways	Details
MDB - Metalloprotein Database	. Protein-Compound Interactions	Details	Free
MEROPS - MEROPS Peptidase Database	. Protein Sequence Focused	Details	Free
Predictome - Predictome	. Protein-Protein Interactions	Details	Free
MPB - Metabolic Pathways of Biochemistry	. Metabolic Pathways . Pathway Diagrams	Details	Free
MycoPathPD - Human Fungal Pathogens Proteome Database	. Protein-Protein Interactions	Details
ORDB - Olfactory Receptor Database	. Protein-Compound Interactions . Protein Sequence Focused	Details	Free
Pathcalling - Curagen Pathcalling	. Protein-Protein Interactions	Details
PIMRider - Protein Interaction Map - Hybrigenics	. Protein-Protein Interactions	Details		PSI-MI
PombePD - Schizosaccharomyces pombe Proteome Database	. Protein-Protein Interactions	Details
ProChart - ProChart database of signal transduction pathway information	. Protein-Protein Interactions	Details
ProNet - Protein-protein Interaction Database	. Protein-Protein Interactions	Details
HumanPSD - Human Proteome Survey Database	. Protein-Protein Interactions	Details
REBASE - Restriction Enzyme Database	. Protein Sequence Focused	Details	Free
Relibase - Protein-ligand database query tool	. Protein-Compound Interactions	Details
SPIN-PP - Surface Properties of Interfaces - Protein-Protein Interfaces	. Protein-Protein Interactions	Details
STKE - Signal Transduction Knowledge Environment	. Signaling Pathways	Details		SBML
WormPD - Caenorhabditis elegans Proteome Database	. Protein-Protein Interactions	Details
YPD - Yeast Proteome Database	. Protein-Protein Interactions	Details
ASEdb - Alanine Scanning Energetics Database	. Protein-Protein Interactions	Details	Free
BBID - Biological Biochemical Image Database	. Pathway Diagrams	Details	Free
BMPH - Boehringer Mannheim Biochemical Pathways Wall Chart	. Pathway Diagrams	Details	Free
COPE - Cytokines and Cells Online Pathfinder Encyclopedia	. Signaling Pathways	Details	Free
PhosphoSite - Cell Signaling Technology's PhosphoSite Database	. Protein-Protein Interactions . Signaling Pathways	Details
NetBiochem - Medical Biochemistry Resource	. Metabolic Pathways . Pathway Diagrams	Details	Free
SPAD - Signaling Pathway Database	. Signaling Pathways . Pathway Diagrams	Details	Free
ASPD - Artificial Selected Proteins/Peptides Database	. Protein-Protein Interactions	Details	Free
TGDB - Tumor Gene Database	. Protein Sequence Focused	Details	Free
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule Pages	. Protein-Protein Interactions . Signaling Pathways	Details	Free	BioPAX
CellML Repository - CellML Model Repository	. Metabolic Pathways . Signaling Pathways	Details	Free	CellML
SBML Model Repository - SBML Model Repository	. Metabolic Pathways . Signaling Pathways	Details		SBML
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins	. Protein-Protein Interactions	Details	Free
AllFuse - Functional Associations of Proteins in Complete Genomes	. Protein-Protein Interactions	Details
PPIV (FANTOM) - RIKEN FANTOM Protein Protein Interaction Viewer	. Protein-Protein Interactions	Details
Malaria - Malaria Parasite Metabolic Pathways	. Metabolic Pathways . Pathway Diagrams	Details	Free
BID - Binding Interface Database	. Protein-Protein Interactions	Details	Free
JASPAR - JASPAR Transcription Factor Binding Profile Database	. Transcription Factors / Gene Regulatory Networks	Details	Free
MedGene - MedGene	Details
PathArt - Pathway Articulator	. Metabolic Pathways . Signaling Pathways	Details
Pathways Knowledge Base - Ingenuity Pathways Knowledge Base	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways . Transcription Factors / Gene Regulatory Networks . Protein-Compound Interactions	Details
GenePath - GenePath	. Genetic Interaction Networks	Details	Free
Reactome - Reactome KnowledgeBase	. Metabolic Pathways . Signaling Pathways	Details	Free	BioPAX SBML
TCDB - Transport Classification Database	Details	Free
TransportDB - TransportDB	Details	Free
IntEnz - Integrated relational Enzyme database	. Metabolic Pathways	Details	Free
NetPro - Molecular Connections NetPro	. Protein-Protein Interactions	Details
GPCR-PD - G protein-coupled receptors protein database	. Protein-Protein Interactions	Details
eMIM - Electronic Molecular Interaction Map	. Signaling Pathways . Pathway Diagrams	Details	Free
INTERACT - INTERACT Protein-protein interaction database	. Protein-Protein Interactions	Details
IntAct - IntAct	. Protein-Protein Interactions	Details	Free	PSI-MI
SPiD - Subtilis Protein interaction Database	. Protein-Protein Interactions	Details	Free
ProMesh - ProMesh Protein-Protein Interaction Database	. Protein-Protein Interactions	Details
HSV1 PPI - Protein-Protein Interactions Table for Human herpesvirus 1	. Protein-Protein Interactions	Details	Free
GroEL PPI - Proteins that interact with GroEL and factors that affect their release	. Protein-Protein Interactions	Details
DPIDB - DNA-Protein Interaction Database	. Protein-Compound Interactions	Details	Free
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge Base	. Metabolic Pathways . Pathway Diagrams	Details	Free
Scansite - Scansite	. Protein-Protein Interactions	Details	Free
PID - NCI-Nature Pathway Interaction Database	. Signaling Pathways . Pathway Diagrams	Details	Free	BioPAX
FlyNets - FlyNets	. Protein-Protein Interactions	Details
PINdb - Proteins Interacting in the Nucleus database	. Protein-Protein Interactions	Details	Free
PQS - Protein Quaternary Structure database	. Protein-Protein Interactions	Details	Free
Prolinks - Prolinks	. Protein-Protein Interactions	Details	Free
InterDom - Database of Interacting Domains	. Protein-Protein Interactions	Details
FusionDB - Prokaryote Gene Fusion Events	. Protein-Protein Interactions	Details	Free
PPID - Protein-Protein Interaction Database	. Protein-Protein Interactions	Details	Free
PDSP Ki Database - Psychoactive Drug Screening Program Ki Database	. Protein-Compound Interactions	Details	Free
TTD - Therapeutic Target Database	. Protein-Compound Interactions	Details	Free
DSM - Dynamic Signaling Maps	. Protein-Protein Interactions . Signaling Pathways . Pathway Diagrams	Details
SCPD - The Promoter Database of Saccharomyces cerevisiae	. Transcription Factors / Gene Regulatory Networks	Details
MetaCore - MetaCore pathway database	. Metabolic Pathways . Signaling Pathways	Details
DOQCS - Database of Quantitative Cellular Signaling	. Signaling Pathways	Details	Free	SBML
Sentra - Sentra Signal Transduction Database	. Signaling Pathways . Protein Sequence Focused	Details
Interolog - Interolog/Regulog Database	. Protein-Protein Interactions . Transcription Factors / Gene Regulatory Networks	Details	Free
AANT - Amino Acid-Nucleotide Interaction Database	Details
ProNIT - Thermodynamic Database for Protein-Nucleic Acid Interactions	Details
ROSPath - Reactive Oxygen Species related Signaling Pathway	. Signaling Pathways	Details
Phospho.ELM - Post-translational phosphorylation database	. Protein-Protein Interactions	Details	Free
KNIFE - Drosophila pattern formation knowledge base	. Genetic Interaction Networks	Details
PRODORIC - Prokaryotic database of gene regulation	. Transcription Factors / Gene Regulatory Networks	Details
STCDB - Signal Transduction Classification Database	. Signaling Pathways	Details	Free
DDIB - Database of Domain Interactions and Bindings	. Protein-Protein Interactions	Details	Free
INOH - Integrating Network Objects with Hierarchies	. Signaling Pathways . Pathway Diagrams	Details	Free	BioPAX
HP-DPI - Helicobacter pylori Database of Protein Interactomes	. Protein-Protein Interactions	Details	Free
POINT - Prediction of Interactome	. Protein-Protein Interactions	Details	Free
iHOP - Information Hyperlinked Over Proteins	Details	Free
ProcessDB - ProcessDB	. Metabolic Pathways . Signaling Pathways	Details
Monod - Modeler's Notebook and Datastore	. Metabolic Pathways . Signaling Pathways	Details	Free
HIV-1 at NCBI - HIV-1, Human Protein Interaction Database at NCBI	. Protein-Protein Interactions	Details	Free
ASC - Active Sequences Collection	. Protein Sequence Focused	Details	Free
ResNet - ResNet	. Protein-Protein Interactions . Signaling Pathways . Protein-Compound Interactions	Details
GenMAPP - Gene MicroArray Pathway Profiler	. Metabolic Pathways . Signaling Pathways	Details	Free
KiBank - KiBank	. Protein-Compound Interactions	Details	Free
Ligand Expo - Ligand Expo	. Protein-Compound Interactions	Details	Free
TRMP - Therapeutically Relevant Multiple Pathways Database	. Signaling Pathways . Pathway Diagrams	Details
CLiBE - Computed Ligand Binding Energy	. Protein-Compound Interactions	Details	Free
KDBI - Kinetic Data of Bio-molecular Interactions database	. Protein-Protein Interactions	Details
Nicholson Minimaps - IUBMB-Nicholson Minimaps	. Metabolic Pathways . Pathway Diagrams	Details	Free
HPID - Human Protein Interaction Database	. Protein-Protein Interactions	Details	Free
PDZBase - PDZ domain protein-protein interaction database	. Protein-Protein Interactions	Details	Free
PRID - Protein-RNA Interaction Database	Details	Free
BioSilico - BioSilico	. Metabolic Pathways	Details
DopaNet - DopaNet	. Protein-Protein Interactions	Details
PANTHER - Protein ANalysis THrough Evolutionary Relationships	. Signaling Pathways . Pathway Diagrams . Protein Sequence Focused	Details	Free	BioPAX SBML
MAPPER - MAPPER	. Transcription Factors / Gene Regulatory Networks	Details
TRACTOR_DB - TRACTOR_DB	. Transcription Factors / Gene Regulatory Networks	Details	Free
TRED - Transcriptional Regulatory Element Database	. Transcription Factors / Gene Regulatory Networks	Details	Free
Precise - Predicted and Consensus Interaction Sites in Enzymes	Details	Free
PDB-Ligand - PDB-Ligand	. Protein-Compound Interactions	Details	Free
MRAD - Metabolic Reaction Analysis Database	. Metabolic Pathways	Details
I2D - Interologous Interaction Database	. Protein-Protein Interactions	Details		PSI-MI
CTD - Comparative Toxicogenomics Database	. Protein-Compound Interactions	Details
XPD - Phosphorylation Site Database	. Signaling Pathways . Protein Sequence Focused	Details	Free
3DID - 3D interacting domains	. Protein-Protein Interactions	Details	Free
PLD - Protein Ligand Database	. Protein-Compound Interactions	Details	Free
PSIbase - Protein Structural Interactome Database	. Protein-Protein Interactions	Details	Free
Interfaces - DATASET OF PROTEIN-PROTEIN INTERFACES	. Protein-Protein Interactions	Details	Free
TECR - Thermodynamics of Enzyme-Catalyzed Reactions	. Metabolic Pathways	Details	Free
SCOPEC - Database of protein catalytic domains	. Protein Sequence Focused	Details
BioModels - BioModels Database	. Metabolic Pathways . Signaling Pathways	Details	Free	BioPAX SBML CellML
KinaseDB - Kinase Pathway Database	. Protein-Protein Interactions	Details	Free
Doodle - Database of oligomerization domains from lambda experiments	. Protein-Protein Interactions	Details	Free
PIBASE - PIBASE	. Protein-Protein Interactions	Details	Free
CTDB - Calmodulin Target Database	. Protein-Protein Interactions	Details	Free
GON - Genomic Object Net	. Signaling Pathways	Details	Free
HiMAP - Human Interactome Map	. Protein-Protein Interactions	Details
Protein Lounge - Protein Lounge	. Metabolic Pathways . Signaling Pathways . Pathway Diagrams	Details
PathCase - CASE Pathways Database System	. Metabolic Pathways	Details	Free	BioPAX
iPath - Invitrogen iPath	. Metabolic Pathways . Signaling Pathways . Pathway Diagrams	Details	Free
GTDB - Glycosylation Pathways Database	. Pathway Diagrams	Details	Free
BioPathway Visualizer - Arizona BioPathway Visualizer	. Transcription Factors / Gene Regulatory Networks	Details	Free
CSP - Cytokine Signaling Pathway Database	. Protein-Protein Interactions	Details
CST - Cell Signaling Technology Pathway Database	. Signaling Pathways . Pathway Diagrams	Details	Free
Biopath - Biochemical Pathways database	. Metabolic Pathways	Details
iPfam - Protein families database of alignments and HMMs	. Protein-Protein Interactions	Details
PUMA2 - Evolutionary Analysis of Metabolism	. Metabolic Pathways	Details	Free
The SEED -	. Metabolic Pathways	Details	Free
LSPD - The Liver Specific Gene Promoter Database	. Transcription Factors / Gene Regulatory Networks	Details	Free
miRNAMap - MicroRNA Map	. Transcription Factors / Gene Regulatory Networks	Details	Free
microrna.org - Microrna.org target database	. Transcription Factors / Gene Regulatory Networks	Details	Free
JWS Online - Online Cellular Systems Modelling	. Metabolic Pathways . Signaling Pathways	Details	Free	SBML
DBTGR - DataBase of Tunicate Gene Regulation	. Transcription Factors / Gene Regulatory Networks	Details	Free
AffinDB - Affinity database for protein-ligand complexes	. Protein-Compound Interactions	Details	Free
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks Gateway	. Protein-Protein Interactions . Signaling Pathways . Transcription Factors / Gene Regulatory Networks	Details	Free
YEASTRACT - YEAst Search for Transcriptional Regulators And Consensus Tracking	. Transcription Factors / Gene Regulatory Networks	Details	Free
SCOPPI - Structural classification of protein–protein interfaces	. Protein-Protein Interactions	Details	Free
iMOTdb - Interacting motifs in proteins database	. Protein-Protein Interactions	Details	Free
PINT - Protein–protein Interactions Thermodynamic Database	. Protein-Protein Interactions	Details	Free
NPInter - Noncoding RNAs and protein related biomacromolecules interaction database	Details	Free
miRBase - microRNA Database	. Transcription Factors / Gene Regulatory Networks	Details	Free
MeRNA - Metals in RNA	Details	Free
Argonaute - Gene regulation by mammalian micro-RNAs	. Transcription Factors / Gene Regulatory Networks	Details	Free
MPromDb - Mammalian Promoter Database	. Transcription Factors / Gene Regulatory Networks	Details
HTPSELEX - HTPSELEX	. Transcription Factors / Gene Regulatory Networks	Details	Free
HemoPDB - Hematopoiesis Promoter Database	. Transcription Factors / Gene Regulatory Networks	Details
cisRED - Cis-regulatory element database	. Transcription Factors / Gene Regulatory Networks	Details	Free
ABS - Annotated regulatory Binding Sites	. Transcription Factors / Gene Regulatory Networks	Details	Free
CA1Neuron - Pathways of the hippocampal CA1 neuron	. Protein-Protein Interactions . Signaling Pathways	Details	Free
ERGO - ERGO Genome Analysis and Discovery System	. Metabolic Pathways	Details
Drastic - Database Resource for Analysis of Signal Transduction In Cells	. Pathway Diagrams	Details
DrugBank - DrugBank	. Protein-Compound Interactions	Details	Free
Ulysses - Projection of Protein Networks across Species	. Protein-Protein Interactions	Details	Free
Cancer Cell Map - The Cancer Cell Map	. Protein-Protein Interactions . Signaling Pathways	Details	Free	BioPAX
Hedgehog - Hedgehog Signaling Pathway Database	. Signaling Pathways . Pathway Diagrams . Transcription Factors / Gene Regulatory Networks	Details
HCNet - Heart and Calcium Functional Network Database	Details	Free
SABIO-RK - SABIO-Reaction Kinetics Database	. Metabolic Pathways	Details	Free	SBML
RiceCyc - The rice metabolic pathway database	. Metabolic Pathways	Details	Free
PathFinder - Cell Signaling Pathways	. Pathway Diagrams	Details	Free
Pathway Slides - Cell Signaling Pathway Slides & Charts	. Pathway Diagrams	Details	Free
MiMI - Michigan Molecular Interactions	. Protein-Protein Interactions . Pathway Diagrams	Details	Free
ECRbase - Evolutionary conserved region database	. Transcription Factors / Gene Regulatory Networks	Details	Free
UniHI - Unified Human Interactome	. Protein-Protein Interactions	Details	Free
PSP - Polygenic signaling pathways	. Protein Sequence Focused	Details	Free
MetNetDB - Metabolic Network Exchange	. Metabolic Pathways	Details	Free
PepBank - PepBank Peptide Database	. Protein-Protein Interactions	Details	Free
SIGMA-ALDRICH - Cell Signalling Pathway Slides & Charts	. Signaling Pathways . Pathway Diagrams . Protein-Compound Interactions	Details	Free
WikiPathways - WikiPathways	. Metabolic Pathways . Signaling Pathways . Pathway Diagrams	Details	Free
gpDB - A Database of G-Proteins and their Interaction with GPCRs	. Protein-Protein Interactions	Details	Free
DOMINO - Domain Peptide Interactions Database	. Protein-Protein Interactions	Details	Free
CellCircuits - CellCircuits	. Protein-Protein Interactions	Details	Free
AthaMap - AthaMap	. Transcription Factors / Gene Regulatory Networks	Details	Free
PROTCOM - Database of Protein Complexes	. Protein-Protein Interactions	Details	Free
SYSTOMONAS - SYSTems biology of pseudOMONAS	. Metabolic Pathways . Transcription Factors / Gene Regulatory Networks	Details	Free	SBML
HMDB - Human Metabolome Database	. Metabolic Pathways	Details	Free
PATRIC - PathoSystems Resource Integration Center	. Metabolic Pathways . Protein Sequence Focused	Details	Free
SNAPPI-DB - Structures, iNterfaces and Alignments for Protein-Protein Interactions	. Protein-Protein Interactions	Details	Free
T1DBase - Type 1 Diabetes Database	. Pathway Diagrams . Protein Sequence Focused	Details	Free
IMG - Integrated Microbial Genomes	. Metabolic Pathways . Protein Sequence Focused	Details	Free
TPDB - Target Protein Database	. Protein-Compound Interactions	Details	Free
CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory Networks	. Transcription Factors / Gene Regulatory Networks	Details	Free
PhosphoPOINT - PhosphoPOINT	. Protein-Protein Interactions	Details	Free
GLIDA - GPCR-Ligand Database	. Protein-Compound Interactions	Details	Free
Binding MOAD - Binding Mother of all Databases	. Protein-Compound Interactions	Details	Free
PDBbind - PDBbind	. Protein-Compound Interactions	Details
HDBase - Huntington's Disease Base	. Protein-Protein Interactions	Details	Free
P.R.I.S.M. - Protein Interactions by Structural Matching	. Protein-Protein Interactions	Details	Free
InterPare - The Protein Interfaceome Database	. Protein-Protein Interactions	Details	Free
PlantCARE - Plant Cis-Acing Regulatory Elements	. Transcription Factors / Gene Regulatory Networks	Details
AGRIS - Arabidopsis Gene Regulatory Information Server	. Transcription Factors / Gene Regulatory Networks	Details	Free
Athena - Athena	. Transcription Factors / Gene Regulatory Networks	Details	Free
DIMA - Domain Interaction Map	. Protein-Protein Interactions	Details	Free
PRIME - Protein interaction and molecular information database	. Protein-Protein Interactions	Details	Free
InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways	. Protein-Protein Interactions . Signaling Pathways	Details	Free	PSI-MI
REDfly - Regulatory Element Database for Drosophila	. Transcription Factors / Gene Regulatory Networks	Details
SGD Pathway Tools - Saccharomyces Genome Database Pathway Tools	. Metabolic Pathways	Details	Free	BioPAX
RGD - Rat Genome Database pathway resource	. Metabolic Pathways . Signaling Pathways	Details	Free
PlantCyc - Plant enzymes and biochemical pathways database	. Metabolic Pathways	Details	Free	BioPAX
MouseCyc - Mouse Pathway Database	. Metabolic Pathways	Details	Free	BioPAX
ITFP - Intergrated Transcription Factor Platform	. Transcription Factors / Gene Regulatory Networks	Details	Free
GO - Gene Ontology	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways	Details	Free
MPIDB - Microbial Protein Interaction Database	. Protein-Protein Interactions	Details	Free
AraCyc - Arabidopsis enzymes and biochemical pathways database	. Metabolic Pathways	Details	Free
CPDB - ConsensusPathDB	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways . Transcription Factors / Gene Regulatory Networks . Protein-Compound Interactions	Details		BioPAX
PDTD - Potential Drug Target Database	. Protein-Compound Interactions	Details	Free
HuPI - database of the Human Proteotheque Initiative	. Protein-Protein Interactions	Details	Free
Interactome - Krogan Lab Interactome Database	. Protein-Protein Interactions . Genetic Interaction Networks	Details	Free
PTM-Switchboard - Post-Translational Modification-Switchboard	. Transcription Factors / Gene Regulatory Networks	Details	Free
UniPROBE - Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation	. Protein-Compound Interactions	Details	Free
miRecords - miRecords	. Transcription Factors / Gene Regulatory Networks	Details	Free
sRNAMap - Small noncoding RNA Map	. Protein-Compound Interactions	Details	Free
TarBase - TarBase	. Transcription Factors / Gene Regulatory Networks . Protein-Compound Interactions	Details	Free
SuperSite - SuperSite	. Protein-Compound Interactions	Details	Free
PIG - Pathogen Interaction Gateway	. Protein-Protein Interactions	Details	Free
PiSITE - Database of Protein Interaction SITEs	. Protein-Protein Interactions	Details	Free
RsiteDB - RNA binding sites data base	. Protein-Compound Interactions	Details	Free
EciD - E. coli Interaction Database	. Protein-Protein Interactions	Details	Free
PIPs - Human Protein-Protein Interaction Prediction	. Protein-Protein Interactions	Details	Free
VirHostNet - Virus-Host Network	. Protein-Protein Interactions . Pathway Diagrams	Details	Free
ExPASy Biochemical Pathways - ExPASy - Roche Applied Science Biochemical Pathways	. Metabolic Pathways	Details	Free
Arabidopsis Reactome - A curated knowledgebase of plant biological pathways	. Metabolic Pathways . Signaling Pathways . Pathway Diagrams	Details	Free	BioPAX SBML
PC - Pathway Commons	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways . Protein-Compound Interactions	Details	Free	PSI-MI BioPAX
TFe - Transcription Factor encyclopedia	. Transcription Factors / Gene Regulatory Networks	Details	Free
MotifMap - MotifMap	. Transcription Factors / Gene Regulatory Networks . Protein Sequence Focused	Details	Free
NURSA - Nuclear Receptor Signaling Atlas	. Protein-Protein Interactions . Protein-Compound Interactions	Details	Free
Millipore Pathways - Your online source for visualizing metabolic and signaling pathways	. Metabolic Pathways . Signaling Pathways	Details	Free
MatrixDB - Extracellular matrix interactions database	. Protein-Protein Interactions . Protein-Compound Interactions	Details	Free	PSI-MI
PSMDB - Protein / Small-molecule database	. Protein-Compound Interactions	Details	Free
iRefWeb - Interaction Reference Index Web Interface	. Protein-Protein Interactions	Details	Free	PSI-MI
iRefIndex - Interaction Reference Index	. Protein-Protein Interactions	Details	Free	PSI-MI
Yeast consensus metabolic network - A consensus reconstruction of yeast metabolism	. Protein-Protein Interactions . Metabolic Pathways . Protein-Compound Interactions	Details	Free	SBML
HCPIN - Human Cancer Protein Interaction Network	. Protein-Protein Interactions . Signaling Pathways	Details	Free
InteroPorc - Automatic molecular interaction predictions	. Protein-Protein Interactions	Details	Free	PSI-MI
RKD - Rice Kinase Database	. Protein-Protein Interactions	Details	Free
BIPA - Biological Interaction database for Protein-nucleic Acid	. Protein-Compound Interactions	Details	Free
HDR - Homeodomain Resource Database	. Protein Sequence Focused	Details	Free
MycoRegNet - Mycobacterial transcription factors and regulatory networks	. Transcription Factors / Gene Regulatory Networks	Details	Free
ADAN - Prediction of protein-protein interaction of modular domains	. Protein-Protein Interactions	Details	Free
Rhea - Reaction database	Details	Free	BioPAX
SMPDB - Small Molecule Pathway Database	. Metabolic Pathways . Signaling Pathways	Details	Free
PepX - Peptide compleXes	. Protein-Compound Interactions	Details	Free
STITCH - Chemical-Protein Interactions	. Protein-Compound Interactions	Details	Free
HAPPI - Human Annotated and Predicted Protein Interaction Database	. Protein-Protein Interactions	Details	Free	PSI-MI
NetPath - NetPath	. Signaling Pathways	Details	Free	PSI-MI BioPAX SBML
HumanCyc - Encyclopedia of Homo sapiens genes and metabolism	. Metabolic Pathways . Pathway Diagrams	Details		BioPAX SBML
SPIKE - Signaling Pathway Integrated Knowledge Engine	. Signaling Pathways . Pathway Diagrams	Details		BioPAX
APID - Agile Protein Interaction DataAnalyzer	. Protein-Protein Interactions	Details	Free
MIPS-MPPI - MIPS Mammalian Protein-Protein Interaction Database	. Protein-Protein Interactions	Details	Free	PSI-MI
SignaLink - SignaLink: a signaling pathway resource	. Signaling Pathways . Pathway Diagrams	Details		SBML
ComSim - Database of protein structures in bound (Complex) and unbound (Single) states	. Protein-Protein Interactions . Protein-Compound Interactions	Details	Free
CORUM - Comprehensive resource of mammalian protein complexes	. Protein-Protein Interactions	Details	Free	PSI-MI
GWIDD - Genome-WIde protein Docking Database	. Protein-Protein Interactions	Details	Free
HRTBLDb - Hormone Receptor Target Binding Loci Database	. Transcription Factors / Gene Regulatory Networks . Protein-Compound Interactions	Details	Free
BioDrugScreen - A Docking Resource for Structure-Based Computational Drug Design	. Protein-Compound Interactions	Details
T3DB - Toxin and Toxin-Target Database	. Protein-Compound Interactions	Details	Free
NCBI BioSystems - NCBI BioSystems	. Metabolic Pathways . Signaling Pathways . Pathway Diagrams . Protein Sequence Focused	Details	Free
MetExplore -	. Metabolic Pathways	Details	Free	SBML
BiGG Knowledgebase -	. Metabolic Pathways	Details		SBML
AtPID - Arabidopsis thaliana Protein Interactome Database	. Protein-Protein Interactions	Details	Free
MetaCrop -	. Metabolic Pathways	Details	Free	SBML
CORNET - CORrelation NETworks	. Protein-Protein Interactions	Details	Free
PathoPlant -	. Signaling Pathways	Details	Free
GeneMANIA - GeneMANIA	. Protein-Protein Interactions . Metabolic Pathways . Signaling Pathways . Pathway Diagrams . Transcription Factors / Gene Regulatory Networks . Genetic Interaction Networks	Details	Free