Pathguide: the pathway resource list
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Complete Listing of All Pathguide Resources

Pathguide contains information about 325 biological pathway related resources and molecular interaction related resources. Click on a link to go to the resource home page or 'Details' for a description page. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

If you know of a pathway resource that is not listed here, or have other questions or comments, please send us an e-mail.

News
New visual navigation May.2010
Click the 'Database interactions' link on the left menu to access.
Major update
All resources were recently reviewed and many new ones were added
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Detailed Pathguide resource statistics now available
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Protein-Protein Interactions  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
3DID - 3D interacting domainsDetails
Free
ADAN - Prediction of protein-protein interaction of modular domainsDetails
Free
AllFuse - Functional Associations of Proteins in Complete GenomesDetailsUnavailable
aMAZE - Protein Function and Biochemical Pathways ProjectDetails
Free
APID - Agile Protein Interaction DataAnalyzerDetails
Free
ASEdb - Alanine Scanning Energetics DatabaseDetails
Free
ASPD - Artificial Selected Proteins/Peptides DatabaseDetails
Free
AtPID - Arabidopsis thaliana Protein Interactome DatabaseDetails
Free
BID - Binding Interface DatabaseDetails
Free
BIND - Biomolecular Interaction Network DatabaseDetails
Free
PSI-MI
BioGRID - Biological General Repository for Interaction DatasetsDetailsAcademic
PSI-MI
BRITE - Biomolecular Relations in Information Transmission and ExpressionDetails
Free
CA1Neuron - Pathways of the hippocampal CA1 neuronDetails
Free
Cancer Cell Map - The Cancer Cell MapDetails
Free
BioPAX
CellCircuits - CellCircuitsDetails
Free
ComSim - Database of protein structures in bound (Complex) and unbound (Single) statesDetails
Free
CORNET - CORrelation NETworksDetails
Free
CORUM - Comprehensive resource of mammalian protein complexesDetails
Free
PSI-MI
CPDB - ConsensusPathDBDetailsAcademic
BioPAX
CSP - Cytokine Signaling Pathway DatabaseDetailsUnavailable
CTDB - Calmodulin Target DatabaseDetails
Free
DDIB - Database of Domain Interactions and BindingsDetails
Free
DIMA - Domain Interaction MapDetails
Free
DIP - Database of Interacting ProteinsDetailsAcademic
PSI-MI
DOMINO - Domain Peptide Interactions DatabaseDetails
Free
Doodle - Database of oligomerization domains from lambda experimentsDetails
Free
DopaNet - DopaNetDetailsUnavailable
DRC - Database of Ribosomal Crosslinks Details
Free
DroID - Drosophila Protein Interaction Map DatabaseDetails
Free
DSM - Dynamic Signaling MapsDetailsLicense
EciD - E. coli Interaction DatabaseDetails
Free
FIMM - Functional Molecular ImmunologyDetailsUnavailable
FusionDB - Prokaryote Gene Fusion EventsDetails
Free
GeneMANIA - GeneMANIADetails
Free
GO - Gene OntologyDetails
Free
GPCR-PD - G protein-coupled receptors protein databaseDetailsLicense
gpDB - A Database of G-Proteins and their Interaction with GPCRsDetails
Free
GroEL PPI - Proteins that interact with GroEL and factors that affect their releaseDetailsUnavailable
GWIDD - Genome-WIde protein Docking DatabaseDetails
Free
HAPPI - Human Annotated and Predicted Protein Interaction DatabaseDetails
Free
PSI-MI
HCPIN - Human Cancer Protein Interaction NetworkDetails
Free
HDBase - Huntington's Disease BaseDetails
Free
HiMAP - Human Interactome MapDetailsAcademic
HIV-1 at NCBI - HIV-1, Human Protein Interaction Database at NCBIDetails
Free
HIVMID - HIV Molecular Immunology DatabaseDetails
Free
HP-DPI - Helicobacter pylori Database of Protein InteractomesDetails
Free
HPID - Human Protein Interaction DatabaseDetails
Free
HPRD - Human Protein Reference Database DetailsAcademic
PSI-MI
HSV1 PPI - Protein-Protein Interactions Table for Human herpesvirus 1Details
Free
HumanPSD - Human Proteome Survey Database DetailsLicense
HuPI - database of the Human Proteotheque InitiativeDetails
Free
I2D - Interologous Interaction DatabaseDetailsAcademic
PSI-MI
ICBS - Inter-Chain Beta-SheetsDetails
Free
iMOTdb - Interacting motifs in proteins databaseDetails
Free
InnateDB - A Knowledge Resource for Innate Immunity Interactions and PathwaysDetails
Free
PSI-MI
IntAct - IntActDetails
Free
PSI-MI
Interactome - Krogan Lab Interactome DatabaseDetails
Free
InterDom - Database of Interacting DomainsDetailsAcademic
Interfaces - DATASET OF PROTEIN-PROTEIN INTERFACESDetails
Free
Interolog - Interolog/Regulog DatabaseDetails
Free
InteroPorc - Automatic molecular interaction predictionsDetails
Free
PSI-MI
InterPare - The Protein Interfaceome DatabaseDetails
Free
iPfam - Protein families database of alignments and HMMsDetailsUnavailable
iRefIndex - Interaction Reference IndexDetails
Free
PSI-MI
iRefWeb - Interaction Reference Index Web InterfaceDetails
Free
PSI-MI
JenPep - JenPep Peptide Binding database Details
Free
KDBI - Kinetic Data of Bio-molecular Interactions databaseDetailsAcademic
KinaseDB - Kinase Pathway DatabaseDetails
Free
MatrixDB - Extracellular matrix interactions databaseDetails
Free
PSI-MI
MHCPEP - Database of MHC binding peptidesDetailsUnavailable
MiMI - Michigan Molecular InteractionsDetails
Free
MINT - Molecular Interaction DatabaseDetails
Free
PSI-MI
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
MIPS-MPPI - MIPS Mammalian Protein-Protein Interaction DatabaseDetails
Free
PSI-MI
MPID-T - MHC-Peptide Interaction DatabaseDetails
Free
MPIDB - Microbial Protein Interaction DatabaseDetails
Free
MycoPathPD - Human Fungal Pathogens Proteome DatabaseDetailsLicense
NetPro - Molecular Connections NetProDetailsUnknown
NURSA - Nuclear Receptor Signaling AtlasDetails
Free
ooTFD - Object Oriented Transcription Factors DatabaseDetailsAcademic
P.R.I.S.M. - Protein Interactions by Structural MatchingDetails
Free
Pathcalling - Curagen PathcallingDetailsUnavailable
PathDB - Pathways DatabaseDetailsUnavailable
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDZBase - PDZ domain protein-protein interaction databaseDetails
Free
PepBank - PepBank Peptide DatabaseDetails
Free
Phospho.ELM - Post-translational phosphorylation databaseDetails
Free
PhosphoBase - Database of phosphorylation sitesDetailsUnavailable
PhosphoPOINT - PhosphoPOINTDetails
Free
PhosphoSite - Cell Signaling Technology's PhosphoSite DatabaseDetailsAcademic
PIBASE - PIBASEDetails
Free
PIG - Pathogen Interaction GatewayDetails
Free
PIMRider - Protein Interaction Map - HybrigenicsDetailsLicense
PSI-MI
PINdb - Proteins Interacting in the Nucleus databaseDetails
Free
PINT - Protein–protein Interactions Thermodynamic DatabaseDetails
Free
PIPs - Human Protein-Protein Interaction PredictionDetails
Free
PiSITE - Database of Protein Interaction SITEsDetails
Free
POINT - Prediction of InteractomeDetails
Free
PombePD - Schizosaccharomyces pombe Proteome DatabaseDetailsLicense
PPID - Protein-Protein Interaction DatabaseDetails
Free
PPIV (FANTOM) - RIKEN FANTOM Protein Protein Interaction ViewerDetailsUnavailable
PQS - Protein Quaternary Structure databaseDetails
Free
Predictome - PredictomeDetails
Free
PRIME - Protein interaction and molecular information databaseDetails
Free
ProChart - ProChart database of signal transduction pathway informationDetailsUnavailable
Prolinks - ProlinksDetails
Free
ProMesh - ProMesh Protein-Protein Interaction DatabaseDetailsUnavailable
ProNet - Protein-protein Interaction DatabaseDetailsUnavailable
PROTCOM - Database of Protein ComplexesDetails
Free
PSIbase - Protein Structural Interactome DatabaseDetails
Free
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
PubGene - PubGeneDetails
Free
ResNet - ResNetDetailsLicense
RKD - Rice Kinase DatabaseDetails
Free
S/MARt_DB - The S/MAR transaction DataBaseDetailsAcademic
Scansite - ScansiteDetails
Free
SCOPPI - Structural classification of protein–protein interfacesDetails
Free
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule PagesDetails
Free
BioPAX
SNAPPI-DB - Structures, iNterfaces and Alignments for Protein-Protein InteractionsDetails
Free
SPiD - Subtilis Protein interaction DatabaseDetails
Free
SPIN-PP - Surface Properties of Interfaces - Protein-Protein InterfacesDetailsUnavailable
STRING - Search Tool for the Retrieval of Interacting Genes/ProteinsDetails
Free
SYFPEITHI - Database of MHC Ligands and Peptide MotifsDetailsLicense
Ulysses - Projection of Protein Networks across SpeciesDetails
Free
UniHI - Unified Human InteractomeDetails
Free
VirHostNet - Virus-Host NetworkDetails
Free
WormPD - Caenorhabditis elegans Proteome DatabaseDetailsLicense
Yeast consensus metabolic network - A consensus reconstruction of yeast metabolismDetails
Free
SBML
YPD - Yeast Proteome DatabaseDetailsLicense
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Metabolic Pathways  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
aMAZE - Protein Function and Biochemical Pathways ProjectDetails
Free
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
AraCyc - Arabidopsis enzymes and biochemical pathways database Details
Free
BiGG Knowledgebase - DetailsAcademic
SBML
BioCyc - BioCyc Knowledge LibraryDetailsAcademic
BioPAX
SBML
BioModels - BioModels DatabaseDetails
Free
BioPAX
SBML
CellML
Biopath - Biochemical Pathways databaseDetailsLicense
BioSilico - BioSilicoDetailsUnavailable
BRENDA - BRaunschweig ENzyme DAtabaseDetailsAcademic
CellML Repository - CellML Model RepositoryDetails
Free
CellML
CPDB - ConsensusPathDBDetailsAcademic
BioPAX
EcoCyc - Encyclopedia of E. coli Genes and MetabolismDetailsAcademic
BioPAX
SBML
EMP - Enzymes and Metabolic Pathways DatabaseDetails
Free
ENZYME - Enzyme nomenclature databaseDetails
Free
ERGO - ERGO Genome Analysis and Discovery SystemDetailsAcademic
ExPASy Biochemical Pathways - ExPASy - Roche Applied Science Biochemical PathwaysDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeneNet - Genetic NetworksDetails
Free
GenMAPP - Gene MicroArray Pathway ProfilerDetails
Free
GO - Gene OntologyDetails
Free
GOLD.db - Genomics of Lipid-associated DisordersDetails
Free
HMDB - Human Metabolome DatabaseDetails
Free
HumanCyc - Encyclopedia of Homo sapiens genes and metabolismDetailsAcademic
BioPAX
SBML
IMG - Integrated Microbial GenomesDetails
Free
Indigo - Gene Neighborhoods and Codon UsageDetailsUnavailable
IntEnz - Integrated relational Enzyme databaseDetails
Free
iPath - Invitrogen iPathDetails
Free
JWS Online - Online Cellular Systems ModellingDetails
Free
SBML
KEGG - Kyoto Encyclopedia of Genes and GenomesDetailsAcademic
BioPAX
LIGAND - Molecular building blocks of life in the chemical spaceDetails
Free
Malaria - Malaria Parasite Metabolic PathwaysDetails
Free
MetaCore - MetaCore pathway databaseDetailsLicense
MetaCrop - Details
Free
SBML
MetaCyc - Metabolic Pathway DatabaseDetailsAcademic
BioPAX
SBML
MetExplore - Details
Free
SBML
MetNetDB - Metabolic Network ExchangeDetails
Free
Millipore Pathways - Your online source for visualizing metabolic and signaling pathwaysDetails
Free
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
Monod - Modeler's Notebook and DatastoreDetails
Free
MouseCyc - Mouse Pathway DatabaseDetails
Free
BioPAX
MPB - Metabolic Pathways of BiochemistryDetails
Free
MRAD - Metabolic Reaction Analysis DatabaseDetailsUnavailable
NCBI BioSystems - NCBI BioSystemsDetails
Free
NetBiochem - Medical Biochemistry ResourceDetails
Free
Nicholson Minimaps - IUBMB-Nicholson MinimapsDetails
Free
PathArt - Pathway ArticulatorDetailsLicense
PathCase - CASE Pathways Database SystemDetails
Free
BioPAX
PathDB - Pathways DatabaseDetailsUnavailable
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PATIKA - Pathway Analysis Tool for Integration and Knowledge AcquisitionDetailsAcademic
PATRIC - PathoSystems Resource Integration CenterDetails
Free
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDS - Pathways Database SystemDetailsUnavailable
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge BaseDetails
Free
PlantCyc - Plant enzymes and biochemical pathways databaseDetails
Free
BioPAX
ProcessDB - ProcessDBDetailsLicense
Protein Lounge - Protein LoungeDetailsLicense
PUMA2 - Evolutionary Analysis of MetabolismDetails
Free
Reactome - Reactome KnowledgeBaseDetails
Free
BioPAX
SBML
RGD - Rat Genome Database pathway resourceDetails
Free
RiceCyc - The rice metabolic pathway databaseDetails
Free
SABIO-RK - SABIO-Reaction Kinetics DatabaseDetails
Free
SBML
SBML Model Repository - SBML Model RepositoryDetailsUnavailable
SBML
SGD Pathway Tools - Saccharomyces Genome Database Pathway ToolsDetails
Free
BioPAX
SMPDB - Small Molecule Pathway DatabaseDetails
Free
SoyBase - USDA-ARS Soybean Genetics and Genome DatabaseDetails
Free
SYSTOMONAS - SYSTems biology of pseudOMONASDetails
Free
SBML
TECR - Thermodynamics of Enzyme-Catalyzed ReactionsDetails
Free
The SEED - Details
Free
UM-BBD - Biocatalysis/Biodegradation DatabaseDetails
Free
WikiPathways - WikiPathwaysDetails
Free
WIT - What Is There?DetailsUnavailable
Yeast consensus metabolic network - A consensus reconstruction of yeast metabolismDetails
Free
SBML
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Signaling Pathways  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
BioModels - BioModels DatabaseDetails
Free
BioPAX
SBML
CellML
CA1Neuron - Pathways of the hippocampal CA1 neuronDetails
Free
Cancer Cell Map - The Cancer Cell MapDetails
Free
BioPAX
CellML Repository - CellML Model RepositoryDetails
Free
CellML
COPE - Cytokines and Cells Online Pathfinder EncyclopediaDetails
Free
CPDB - ConsensusPathDBDetailsAcademic
BioPAX
CSNDB - Cell Signaling Networks DatabaseDetailsUnavailable
CST - Cell Signaling Technology Pathway DatabaseDetails
Free
DOQCS - Database of Quantitative Cellular SignalingDetails
Free
SBML
DSM - Dynamic Signaling MapsDetailsLicense
eMIM - Electronic Molecular Interaction MapDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeneNet - Genetic NetworksDetails
Free
GenMAPP - Gene MicroArray Pathway ProfilerDetails
Free
GO - Gene OntologyDetails
Free
GOLD.db - Genomics of Lipid-associated DisordersDetails
Free
GON - Genomic Object NetDetails
Free
HCPIN - Human Cancer Protein Interaction NetworkDetails
Free
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsAcademic
InnateDB - A Knowledge Resource for Innate Immunity Interactions and PathwaysDetails
Free
PSI-MI
INOH - Integrating Network Objects with HierarchiesDetails
Free
BioPAX
iPath - Invitrogen iPathDetails
Free
JWS Online - Online Cellular Systems ModellingDetails
Free
SBML
MetaCore - MetaCore pathway databaseDetailsLicense
Millipore Pathways - Your online source for visualizing metabolic and signaling pathwaysDetails
Free
Monod - Modeler's Notebook and DatastoreDetails
Free
NCBI BioSystems - NCBI BioSystemsDetails
Free
NetPath - NetPathDetails
Free
PSI-MI
BioPAX
SBML
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsDetails
Free
BioPAX
SBML
PathArt - Pathway ArticulatorDetailsLicense
PathDB - Pathways DatabaseDetailsUnavailable
PathoPlant - Details
Free
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PATIKA - Pathway Analysis Tool for Integration and Knowledge AcquisitionDetailsAcademic
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDS - Pathways Database SystemDetailsUnavailable
PhosphoSite - Cell Signaling Technology's PhosphoSite DatabaseDetailsAcademic
PID - NCI-Nature Pathway Interaction DatabaseDetails
Free
BioPAX
ProcessDB - ProcessDBDetailsLicense
Protein Lounge - Protein LoungeDetailsLicense
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
Reactome - Reactome KnowledgeBaseDetails
Free
BioPAX
SBML
ResNet - ResNetDetailsLicense
RGD - Rat Genome Database pathway resourceDetails
Free
ROSPath - Reactive Oxygen Species related Signaling PathwayDetailsUnknown
SBML Model Repository - SBML Model RepositoryDetailsUnavailable
SBML
Sentra - Sentra Signal Transduction DatabaseDetailsAcademic
SIGMA-ALDRICH - Cell Signalling Pathway Slides & ChartsDetails
Free
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule PagesDetails
Free
BioPAX
SignaLink - SignaLink: a signaling pathway resourceDetailsAcademic
SBML
SigPath - Signaling Pathway Information SystemDetails
Free
SMPDB - Small Molecule Pathway DatabaseDetails
Free
SPAD - Signaling Pathway DatabaseDetails
Free
SPIKE - Signaling Pathway Integrated Knowledge EngineDetailsAcademic
BioPAX
STCDB - Signal Transduction Classification DatabaseDetails
Free
STKE - Signal Transduction Knowledge EnvironmentDetailsAcademic
SBML
TRANSPATH - Signal Transduction BrowserDetailsLicense
TRMP - Therapeutically Relevant Multiple Pathways DatabaseDetailsAcademic
TRRD - Transcription Regulatory Regions DatabaseDetails
Free
WikiPathways - WikiPathwaysDetails
Free
XPD - Phosphorylation Site DatabaseDetails
Free
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Pathway Diagrams  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
Arabidopsis Reactome - A curated knowledgebase of plant biological pathwaysDetails
Free
BioPAX
SBML
BBID - Biological Biochemical Image DatabaseDetails
Free
BioCarta - BioCarta Pathway DiagramsDetails
Free
BMPH - Boehringer Mannheim Biochemical Pathways Wall ChartDetails
Free
CST - Cell Signaling Technology Pathway DatabaseDetails
Free
Drastic - Database Resource for Analysis of Signal Transduction In CellsDetailsUnavailable
DSM - Dynamic Signaling MapsDetailsLicense
eMIM - Electronic Molecular Interaction MapDetails
Free
GeneMANIA - GeneMANIADetails
Free
GTDB - Glycosylation Pathways DatabaseDetails
Free
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsAcademic
HPRD - Human Protein Reference Database DetailsAcademic
PSI-MI
HumanCyc - Encyclopedia of Homo sapiens genes and metabolismDetailsAcademic
BioPAX
SBML
INOH - Integrating Network Objects with HierarchiesDetails
Free
BioPAX
iPath - Invitrogen iPathDetails
Free
KEGG - Kyoto Encyclopedia of Genes and GenomesDetailsAcademic
BioPAX
KMIM - Kohn Molecular Interaction MapsDetails
Free
Malaria - Malaria Parasite Metabolic PathwaysDetails
Free
MiMI - Michigan Molecular InteractionsDetails
Free
MIPS CYGD - MIPS Comprehensive Yeast Genome DatabaseDetails
Free
PSI-MI
MPB - Metabolic Pathways of BiochemistryDetails
Free
NCBI BioSystems - NCBI BioSystemsDetails
Free
NetBiochem - Medical Biochemistry ResourceDetails
Free
Nicholson Minimaps - IUBMB-Nicholson MinimapsDetails
Free
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsDetails
Free
BioPAX
SBML
PathFinder - Cell Signaling PathwaysDetails
Free
Pathway Slides - Cell Signaling Pathway Slides & ChartsDetails
Free
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge BaseDetails
Free
PID - NCI-Nature Pathway Interaction DatabaseDetails
Free
BioPAX
Protein Lounge - Protein LoungeDetailsLicense
SIGMA-ALDRICH - Cell Signalling Pathway Slides & ChartsDetails
Free
SignaLink - SignaLink: a signaling pathway resourceDetailsAcademic
SBML
SPAD - Signaling Pathway DatabaseDetails
Free
SPIKE - Signaling Pathway Integrated Knowledge EngineDetailsAcademic
BioPAX
T1DBase - Type 1 Diabetes DatabaseDetails
Free
TRMP - Therapeutically Relevant Multiple Pathways DatabaseDetailsAcademic
VirHostNet - Virus-Host NetworkDetails
Free
WikiPathways - WikiPathwaysDetails
Free
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Transcription Factors / Gene Regulatory Networks  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
ABS - Annotated regulatory Binding SitesDetails
Free
AGRIS - Arabidopsis Gene Regulatory Information ServerDetails
Free
aMAZE - Protein Function and Biochemical Pathways ProjectDetails
Free
Argonaute - Gene regulation by mammalian micro-RNAsDetails
Free
AthaMap - AthaMapDetails
Free
Athena - AthenaDetails
Free
BioPathway Visualizer - Arizona BioPathway VisualizerDetails
Free
cisRED - Cis-regulatory element databaseDetails
Free
COMPEL - Database on Composite Regulatory ElementsDetailsAcademic
CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory NetworksDetails
Free
CPDB - ConsensusPathDBDetailsAcademic
BioPAX
DBTBS - Database of Bacillus subtilis Promoters and Transcription FactorsDetails
Free
DBTGR - DataBase of Tunicate Gene RegulationDetails
Free
DPInteract - DNA-Protein Interactions DatabaseDetails
Free
ECRbase - Evolutionary conserved region databaseDetails
Free
GeneMANIA - GeneMANIADetails
Free
GeNet - Gene Networks DatabaseDetailsUnknown
Hedgehog - Hedgehog Signaling Pathway DatabaseDetailsAcademic
HemoPDB - Hematopoiesis Promoter DatabaseDetailsUnknown
HoxPro - HOX ProDetails
Free
HRTBLDb - Hormone Receptor Target Binding Loci DatabaseDetails
Free
HTPSELEX - HTPSELEXDetails
Free
Interolog - Interolog/Regulog DatabaseDetails
Free
ITFP - Intergrated Transcription Factor PlatformDetails
Free
JASPAR - JASPAR Transcription Factor Binding Profile DatabaseDetails
Free
LSPD - The Liver Specific Gene Promoter DatabaseDetails
Free
MAPPER - MAPPERDetailsAcademic
microrna.org - Microrna.org target databaseDetails
Free
miRBase - microRNA DatabaseDetails
Free
miRecords - miRecordsDetails
Free
miRNAMap - MicroRNA MapDetails
Free
MotifMap - MotifMapDetails
Free
MPromDb - Mammalian Promoter DatabaseDetailsUnknown
MycoRegNet - Mycobacterial transcription factors and regulatory networksDetails
Free
ooTFD - Object Oriented Transcription Factors DatabaseDetailsAcademic
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PlantCARE - Plant Cis-Acing Regulatory ElementsDetailsAcademic
PRODORIC - Prokaryotic database of gene regulationDetailsAcademic
pSTIING - Protein, Signalling, Transcriptional Interactions & Inflammation Networks GatewayDetails
Free
PTM-Switchboard - Post-Translational Modification-SwitchboardDetails
Free
REDfly - Regulatory Element Database for DrosophilaDetailsUnknown
RegulonDB - Database on Transcriptional Regulation and Genome OrganizationDetailsAcademic
SCPD - The Promoter Database of Saccharomyces cerevisiaeDetailsAcademic
SYSTOMONAS - SYSTems biology of pseudOMONASDetails
Free
SBML
TarBase - TarBaseDetails
Free
TFe - Transcription Factor encyclopediaDetails
Free
TRACTOR_DB - TRACTOR_DBDetails
Free
TRANSFAC - Transcription Factor DatabaseDetailsLicense
TRED - Transcriptional Regulatory Element DatabaseDetails
Free
TRRD - Transcription Regulatory Regions DatabaseDetails
Free
YEASTRACT - YEAst Search for Transcriptional Regulators And Consensus TrackingDetails
Free
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Protein-Compound Interactions  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
AffinDB - Affinity database for protein-ligand complexesDetails
Free
Binding MOAD - Binding Mother of all DatabasesDetails
Free
BindingDB - The Binding DatabaseDetails
Free
BioDrugScreen - A Docking Resource for Structure-Based Computational Drug DesignDetailsUnknown
BIPA - Biological Interaction database for Protein-nucleic AcidDetails
Free
CLiBE - Computed Ligand Binding EnergyDetails
Free
ComSim - Database of protein structures in bound (Complex) and unbound (Single) statesDetails
Free
CPDB - ConsensusPathDBDetailsAcademic
BioPAX
CTD - Comparative Toxicogenomics DatabaseDetailsAcademic
DPIDB - DNA-Protein Interaction DatabaseDetails
Free
DrugBank - DrugBankDetails
Free
GLIDA - GPCR-Ligand DatabaseDetails
Free
Het-PDB_Navi - Het-PDB NaviDetails
Free
HRTBLDb - Hormone Receptor Target Binding Loci DatabaseDetails
Free
KiBank - KiBankDetails
Free
Ligand Expo - Ligand ExpoDetails
Free
MatrixDB - Extracellular matrix interactions databaseDetails
Free
PSI-MI
MDB - Metalloprotein DatabaseDetails
Free
NRR - Nuclear Receptor Resource Details
Free
NURSA - Nuclear Receptor Signaling AtlasDetails
Free
ORDB - Olfactory Receptor DatabaseDetails
Free
Pathways Knowledge Base - Ingenuity Pathways Knowledge BaseDetailsLicense
PC - Pathway CommonsDetails
Free
PSI-MI
BioPAX
PDB-Ligand - PDB-LigandDetails
Free
PDBbind - PDBbindDetailsAcademic
PDSP Ki Database - Psychoactive Drug Screening Program Ki DatabaseDetails
Free
PDTD - Potential Drug Target DatabaseDetails
Free
PepX - Peptide compleXesDetails
Free
PLD - Protein Ligand DatabaseDetails
Free
PSMDB - Protein / Small-molecule databaseDetails
Free
Relibase - Protein-ligand database query toolDetailsAcademic
ResNet - ResNetDetailsLicense
RsiteDB - RNA binding sites data baseDetails
Free
SIGMA-ALDRICH - Cell Signalling Pathway Slides & ChartsDetails
Free
sRNAMap - Small noncoding RNA MapDetails
Free
STITCH - Chemical-Protein InteractionsDetails
Free
SuperSite - SuperSiteDetails
Free
T3DB - Toxin and Toxin-Target DatabaseDetails
Free
TarBase - TarBaseDetails
Free
TPDB - Target Protein DatabaseDetails
Free
TTD - Therapeutic Target DatabaseDetails
Free
UniPROBE - Universal Protein Binding Microarray Resource for Oligonucleotide Binding EvaluationDetails
Free
Yeast consensus metabolic network - A consensus reconstruction of yeast metabolismDetails
Free
SBML
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Genetic Interaction Networks  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
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Protein Sequence Focused  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
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Other  
Database Name (Order: alphabetically | by web popularity Note ) Full Record Availability Standards
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Note on Web Popularity:
As indexed by Google, popularity is estimated by the number of web pages that mention each resource's homepage (subtracting links from the resource itself). This number provides a rough indication of the relative popularity of each resource; this should not be interpreted as an accurate measure of resource significance.
There are a number of reasons why a resource may have no links, such as: it may be a very new resource and no pages link to it yet; it may have been recently relocated and no links point to the new location; it may be a private resource and no links point to the brochure page; it may be a defunct resource without a valid link.
Thanks to Robert Hoffmann for help updating the Google ranking.

"Pathguide: the pathway resource list" is maintained by Gary Bader1,2 and Sylva Donaldson2.
The website was originally created by Michael Cary 1 and was significantly updated and redesigned by Vuk Pavlovic2.
Thanks to Emek Demir for the Pathguide name.

1. Sander Group at Memorial Sloan-Kettering Cancer Center
2. Bader Lab

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