Pathguide: the pathway resource list
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Database Interactions

Network

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


Resources
Database Name Categories Full Record Availability Standards
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Legends
Resource Type
Interactions
Pathways
Predictive interactions
Metamining
Exchange format language
Unifying efforts
Not categorized
Interaction Type
Source Mining source data
Source Maps to source
Bidirectional exchange agreement
Back to the Top

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 - Functional Hierarchies and Binary Relationships of Biological Entities . Protein-Protein InteractionsDetails
Free
DIP - Database of Interacting Proteins . Protein-Protein InteractionsDetailsAcademic
PSI-MI
LIGAND - Molecular building blocks of life in the chemical space . Metabolic PathwaysDetails
Free
aMAZE - Protein Function and Biochemical Pathways Project . Protein-Protein Interactions
. Metabolic Pathways
. Transcription Factors / Gene Regulatory Networks
DetailsUnavailable
WIT - What Is There? . Metabolic PathwaysDetailsUnavailable
BioGRID - Biological General Repository for Interaction Datasets . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
PSI-MI
BioCyc - BioCyc Knowledge Library . Metabolic PathwaysDetailsAcademic
BioPAX
SBML
EcoCyc - Encyclopedia of E. coli Genes and Metabolism . Metabolic PathwaysDetailsAcademic
BioPAX
SBML
MetaCyc - Metabolic Pathway Database . Metabolic PathwaysDetailsAcademic
BioPAX
SBML
CSNDB - Cell Signaling Networks Database . Signaling PathwaysDetailsUnavailable
EMP - Enzymes and Metabolic Pathways Database . Metabolic PathwaysDetailsUnavailable
ENZYME - Enzyme nomenclature database . Metabolic PathwaysDetails
Free
HPRD - Human Protein Reference Database . Protein-Protein Interactions
. Pathway Diagrams
DetailsAcademic
PSI-MI
AntiJen - AntiJen a Kinetic, Thermodynamic and Cellular Database . Protein-Protein InteractionsDetails
Free
KEGG - Kyoto Encyclopedia of Genes and Genomes . Metabolic Pathways
. Pathway Diagrams
DetailsAcademic
BioPAX
MINT - Molecular Interaction Database . Protein-Protein InteractionsDetails
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
DetailsAcademic
PathDB - Pathways Database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
DetailsUnavailable
TRANSFAC - Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetailsLicense
Proteome - . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
DetailsLicense
TRRD - Transcription Regulatory Regions Database . Signaling Pathways
. Transcription Factors / Gene Regulatory Networks
Details
Free
ABCdb - Archaea and Bacteria ABC transporter database . Protein Sequence FocusedDetails
Free
BioCarta - BioCarta Pathway Diagrams . Pathway DiagramsDetails
Free
COMPEL - Database on Composite Regulatory Elements . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
DRC - Database of Ribosomal Crosslinks . Protein-Protein InteractionsDetails
Free
FIMM - Functional Molecular Immunology . Protein-Protein InteractionsDetailsUnavailable
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 InteractionsDetails
Free
ICBS - Inter-Chain Beta-Sheets . Protein-Protein InteractionsDetails
Free
KMIM - Kohn Molecular Interaction Maps . Pathway DiagramsDetails
Free
MHCPEP - Database of MHC binding peptides . Protein-Protein InteractionsDetailsUnavailable
MPID-T - MHC-Peptide Interaction Database . Protein-Protein InteractionsDetails
Free
PATIKA - Pathway Analysis Tool for Integration and Knowledge Acquisition . Metabolic Pathways
. Signaling Pathways
DetailsAcademic
PDS - Pathways Database System . Metabolic Pathways
. Signaling Pathways
DetailsUnavailable
PhosphoBase - Database of phosphorylation sites . Protein-Protein Interactions
. Protein Sequence Focused
Details
Free
DroID - Drosophila Protein Interaction Map Database . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
PubGene - PubGene . Protein-Protein InteractionsDetails
Free
RegulonDB - Database on Transcriptional Regulation and Genome Organization . Transcription Factors / Gene Regulatory NetworksDetailsAcademic
BioPAX
SELEX_DB - Randomized DNA/RNA sequence databaseDetails
Free
SoyBase - USDA-ARS Soybean Genetics and Genome Database . Metabolic PathwaysDetails
Free
SYFPEITHI - Database of MHC Ligands and Peptide Motifs . Protein-Protein InteractionsDetailsLicense
UM-BBD - Biocatalysis/Biodegradation Database . Metabolic PathwaysDetails
Free
S/MARt_DB - The S/MAR transaction DataBase . Protein-Protein InteractionsDetailsAcademic
SigPath - Signaling Pathway Information System . Signaling PathwaysDetails
Free
AARSDB - Aminoacyl-tRNA Synthetase Database Details
Free
BindingDB - The Binding Database . Protein-Compound InteractionsDetails
Free
BRENDA - BRaunschweig ENzyme DAtabase . Metabolic PathwaysDetailsAcademic
DBTBS - Database of Bacillus subtilis Promoters and Transcription Factors . Transcription Factors / Gene Regulatory NetworksDetails
Free
DPInteract - DNA-Protein Interactions Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
GeNet - Gene Networks Database . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
HIVMID - HIV Molecular Immunology Database . Protein-Protein InteractionsDetails
Free
HoxPro - HOX Pro . Transcription Factors / Gene Regulatory NetworksDetails
Free
InBase - The Intein Database . Protein Sequence FocusedDetails
Free
Indigo - Gene Neighborhoods and Codon Usage . Metabolic PathwaysDetailsUnavailable
MDB - Metalloprotein Database . Protein-Compound InteractionsDetailsUnavailable
MEROPS - MEROPS Peptidase Database . Protein Sequence FocusedDetails
Free
Predictome - Predictome . Protein-Protein InteractionsDetails
Free
MPB - Metabolic Pathways of Biochemistry . Metabolic Pathways
. Pathway Diagrams
DetailsUnavailable
MycoPathPD - Human Fungal Pathogens Proteome Database . Protein-Protein InteractionsDetailsLicense
ORDB - Olfactory Receptor Database . Protein-Compound Interactions
. Protein Sequence Focused
Details
Free
Pathcalling - Curagen Pathcalling . Protein-Protein InteractionsDetailsUnavailable
PIMRider - Protein Interaction Map - Hybrigenics . Protein-Protein InteractionsDetailsLicense
PSI-MI
PombePD - Schizosaccharomyces pombe Proteome Database . Protein-Protein InteractionsDetailsLicense
ProChart - ProChart database of signal transduction pathway information . Protein-Protein InteractionsDetailsUnavailable
ProNet - Protein-protein Interaction Database . Protein-Protein InteractionsDetailsUnavailable
HumanPSD - Human Proteome Survey Database . Protein-Protein InteractionsDetailsLicense
REBASE - Restriction Enzyme Database . Protein Sequence FocusedDetails
Free
Relibase - Protein-ligand database query tool . Protein-Compound InteractionsDetailsAcademic
SPIN-PP - Surface Properties of Interfaces - Protein-Protein Interfaces . Protein-Protein InteractionsDetailsUnavailable
STKE - Signal Transduction Knowledge Environment . Signaling PathwaysDetailsAcademic
SBML
WormPD - Caenorhabditis elegans Proteome Database . Protein-Protein InteractionsDetailsLicense
YPD - Yeast Proteome Database . Protein-Protein InteractionsDetailsLicense
ASEdb - Alanine Scanning Energetics Database . Protein-Protein InteractionsDetails
Free
BBID - Biological Biochemical Image Database . Pathway DiagramsDetails
Free
BMPH - Boehringer Mannheim Biochemical Pathways Wall Chart . Pathway DiagramsDetails
Free
COPE - Cytokines and Cells Online Pathfinder Encyclopedia . Signaling PathwaysDetails
Free
PhosphoSite - Cell Signaling Technology's PhosphoSite Database . Protein-Protein Interactions
. Signaling Pathways
DetailsAcademic
BioPAX
NetBiochem - Medical Biochemistry Resource . Metabolic Pathways
. Pathway Diagrams
DetailsUnavailable
SPAD - Signaling Pathway Database . Signaling Pathways
. Pathway Diagrams
Details
Free
ASPD - Artificial Selected Proteins/Peptides Database . Protein-Protein InteractionsDetails
Free
TGDB - Tumor Gene Database . Protein Sequence FocusedDetails
Free
Signaling Gateway - UCSD-Nature Signaling Gateway Molecule Pages . Protein-Protein Interactions
. Signaling Pathways
Details
Free
BioPAX
SBML
CellML Repository - CellML Model Repository . Metabolic Pathways
. Signaling Pathways
Details
Free
CellML
SBML Model Repository - SBML Model Repository . Metabolic Pathways
. Signaling Pathways
DetailsUnavailable
SBML
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins . Protein-Protein InteractionsDetailsLicense
AllFuse - Functional Associations of Proteins in Complete Genomes . Protein-Protein InteractionsDetailsUnavailable
PPIV (FANTOM) - RIKEN FANTOM Protein Protein Interaction Viewer . Protein-Protein InteractionsDetailsUnavailable
Malaria - Malaria Parasite Metabolic Pathways . Metabolic Pathways
. Pathway Diagrams
Details
Free
BID - Binding Interface Database . Protein-Protein InteractionsDetails
Free
JASPAR - JASPAR Transcription Factor Binding Profile Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
MedGene - MedGeneDetailsAcademic
PathArt - Pathway Articulator . Metabolic Pathways
. Signaling Pathways
DetailsLicense
Pathways Knowledge Base - Ingenuity Pathways Knowledge Base . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
DetailsLicense
GenePath - GenePath . Genetic Interaction NetworksDetails
Free
Reactome - Reactome KnowledgeBase . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
PSI-MI
BioPAX
SBML
TCDB - Transport Classification DatabaseDetails
Free
TransportDB - TransportDBDetails
Free
IntEnz - Integrated relational Enzyme database . Metabolic PathwaysDetails
Free
NetPro - Molecular Connections NetPro . Protein-Protein InteractionsDetailsLicense
GPCR-PD - G protein-coupled receptors protein database . Protein-Protein InteractionsDetailsLicense
eMIM - Electronic Molecular Interaction Map . Signaling Pathways
. Pathway Diagrams
Details
Free
INTERACT - INTERACT Protein-protein interaction database . Protein-Protein InteractionsDetailsUnavailable
IntAct - IntAct . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
PSI-MI
SPiD - Subtilis Protein interaction Database . Protein-Protein InteractionsDetailsUnavailable
ProMesh - ProMesh Protein-Protein Interaction Database . Protein-Protein InteractionsDetailsUnavailable
HSV1 PPI - Protein-Protein Interactions Table for Human herpesvirus 1 . Protein-Protein InteractionsDetailsUnavailable
GroEL PPI - Proteins that interact with GroEL and factors that affect their release . Protein-Protein InteractionsDetailsUnavailable
DPIDB - DNA-Protein Interaction Database . Protein-Compound InteractionsDetails
Free
PharmGKB - The Pharmacogenetics and Pharmacogenomics Knowledge Base . Metabolic Pathways
. Pathway Diagrams
Details
Free
BioPAX
Scansite - Scansite . Protein-Protein InteractionsDetails
Free
PID - NCI-Nature Pathway Interaction Database . Signaling Pathways
. Pathway Diagrams
Details
Free
BioPAX
FlyNets - FlyNets . Protein-Protein InteractionsDetailsUnavailable
PINdb - Proteins Interacting in the Nucleus database . Protein-Protein InteractionsDetails
Free
PQS - Protein Quaternary Structure database . Protein-Protein InteractionsDetails
Free
Prolinks - Prolinks . Protein-Protein InteractionsDetails
Free
InterDom - Database of Interacting Domains . Protein-Protein InteractionsDetailsAcademic
FusionDB - Prokaryote Gene Fusion Events . Protein-Protein InteractionsDetails
Free
PPID - Protein-Protein Interaction Database . Protein-Protein InteractionsDetailsLicense
PDSP Ki Database - Psychoactive Drug Screening Program Ki Database . Protein-Compound InteractionsDetailsUnavailable
TTD - Therapeutic Target Database . Protein-Compound InteractionsDetails
Free
DSM - Dynamic Signaling Maps . Protein-Protein Interactions
. Signaling Pathways
. Pathway Diagrams
DetailsUnavailable
SCPD - The Promoter Database of Saccharomyces cerevisiae . Transcription Factors / Gene Regulatory NetworksDetailsAcademic
MetaCore - MetaCore pathway database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
. Genetic Interaction Networks
DetailsLicense
BioPAX
SBML
DOQCS - Database of Quantitative Cellular Signaling . Signaling PathwaysDetails
Free
SBML
Sentra - Sentra Signal Transduction Database . Signaling Pathways
. Protein Sequence Focused
DetailsUnavailable
Interolog - Interolog/Regulog Database . Protein-Protein Interactions
. Transcription Factors / Gene Regulatory Networks
Details
Free
AANT - Amino Acid-Nucleotide Interaction DatabaseDetails
Free
ProNIT - Thermodynamic Database for Protein-Nucleic Acid InteractionsDetailsAcademic
ROSPath - Reactive Oxygen Species related Signaling Pathway . Signaling PathwaysDetails
Free
Phospho.ELM - Post-translational phosphorylation database . Protein-Protein InteractionsDetails
Free
KNIFE - Drosophila pattern formation knowledge base . Genetic Interaction NetworksDetailsUnavailable
PRODORIC - Prokaryotic database of gene regulation . Transcription Factors / Gene Regulatory NetworksDetailsAcademic
STCDB - Signal Transduction Classification Database . Signaling PathwaysDetails
Free
DDIB - Database of Domain Interactions and Bindings . Protein-Protein InteractionsDetailsUnavailable
INOH - Integrating Network Objects with Hierarchies . Signaling Pathways
. Pathway Diagrams
Details
Free
BioPAX
HP-DPI - Helicobacter pylori Database of Protein Interactomes . Protein-Protein InteractionsDetails
Free
POINT - Prediction of Interactome . Protein-Protein InteractionsDetails
Free
iHOP - Information Hyperlinked Over ProteinsDetails
Free
ProcessDB - ProcessDB . Metabolic Pathways
. Signaling Pathways
DetailsLicense
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 InteractionsDetails
Free
ASC - Active Sequences Collection . Protein Sequence FocusedDetails
Free
ResNet - ResNet . Protein-Protein Interactions
. Signaling Pathways
. Protein-Compound Interactions
DetailsLicense
GenMAPP - Gene MicroArray Pathway Profiler . Metabolic Pathways
. Signaling Pathways
Details
Free
KiBank - KiBank . Protein-Compound InteractionsDetailsUnavailable
Ligand Expo - Ligand Expo . Protein-Compound InteractionsDetails
Free
TRMP - Therapeutically Relevant Multiple Pathways Database . Signaling Pathways
. Pathway Diagrams
Details
Free
CLiBE - Computed Ligand Binding Energy . Protein-Compound InteractionsDetails
Free
KDBI - Kinetic Data of Bio-molecular Interactions database . Protein-Protein InteractionsDetailsUnavailable
Nicholson Minimaps - IUBMB-Nicholson Minimaps . Metabolic Pathways
. Pathway Diagrams
Details
Free
HPID - Human Protein Interaction Database . Protein-Protein InteractionsDetailsUnavailable
PDZBase - PDZ domain protein-protein interaction database . Protein-Protein InteractionsDetails
Free
PRID - Protein-RNA Interaction DatabaseDetails
Free
BioSilico - BioSilico . Metabolic PathwaysDetailsUnavailable
DopaNet - DopaNet . Protein-Protein InteractionsDetailsUnavailable
PANTHER - Protein ANalysis THrough Evolutionary Relationships . Signaling Pathways
. Pathway Diagrams
. Protein Sequence Focused
Details
Free
BioPAX
SBML
MAPPER - MAPPER . Transcription Factors / Gene Regulatory NetworksDetailsAcademic
TRACTOR_DB - TRACTOR_DB . Transcription Factors / Gene Regulatory NetworksDetails
Free
TRED - Transcriptional Regulatory Element Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
Precise - Predicted and Consensus Interaction Sites in EnzymesDetailsUnavailable
PDB-Ligand - PDB-Ligand . Protein-Compound InteractionsDetailsUnavailable
MRAD - Metabolic Reaction Analysis Database . Metabolic PathwaysDetailsUnavailable
I2D - Interologous Interaction Database . Protein-Protein InteractionsDetailsAcademic
PSI-MI
CTD - Comparative Toxicogenomics Database . Protein-Compound InteractionsDetailsAcademic
XPD - Phosphorylation Site Database . Signaling Pathways
. Protein Sequence Focused
Details
Free
3DID - 3D interacting domains . Protein-Protein InteractionsDetails
Free
PLD - Protein Ligand Database . Protein-Compound InteractionsDetailsUnavailable
PSIbase - Protein Structural Interactome Database . Protein-Protein InteractionsDetails
Free
Interfaces - DATASET OF PROTEIN-PROTEIN INTERFACES . Protein-Protein InteractionsDetails
Free
TECR - Thermodynamics of Enzyme-Catalyzed Reactions . Metabolic PathwaysDetails
Free
SCOPEC - Database of protein catalytic domains . Protein Sequence FocusedDetailsUnavailable
BioModels - BioModels Database . Metabolic Pathways
. Signaling Pathways
Details
Free
BioPAX
SBML
CellML
KinaseDB - Kinase Pathway Database . Protein-Protein InteractionsDetails
Free
Doodle - Database of oligomerization domains from lambda experiments . Protein-Protein InteractionsDetailsUnavailable
PIBASE - PIBASE . Protein-Protein InteractionsDetails
Free
CTDB - Calmodulin Target Database . Protein-Protein InteractionsDetails
Free
GON - Genomic Object Net . Signaling PathwaysDetails
Free
HiMAP - Human Interactome Map . Protein-Protein InteractionsDetailsUnavailable
Protein Lounge - Protein Lounge . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
. Transcription Factors / Gene Regulatory Networks
DetailsLicense
PathCase - CASE Pathways Database System . Metabolic PathwaysDetails
Free
BioPAX
iPath - Invitrogen iPath . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
DetailsUnavailable
GTDB - Glycosylation Pathways Database . Pathway DiagramsDetails
Free
BioPathway Visualizer - Arizona BioPathway Visualizer . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
CSP - Cytokine Signaling Pathway Database . Protein-Protein InteractionsDetailsUnavailable
CST - Cell Signaling Technology Pathway Database . Signaling Pathways
. Pathway Diagrams
Details
Free
Biopath - Biochemical Pathways database . Metabolic PathwaysDetailsLicense
iPfam - Protein families database of alignments and HMMs . Protein-Protein InteractionsDetails
Free
PUMA2 - Evolutionary Analysis of Metabolism . Metabolic PathwaysDetailsUnavailable
The SEED - . Metabolic PathwaysDetails
Free
LSPD - The Liver Specific Gene Promoter Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
miRNAMap - MicroRNA Map . Transcription Factors / Gene Regulatory NetworksDetails
Free
microrna.org - Microrna.org target database . Transcription Factors / Gene Regulatory NetworksDetails
Free
JWS Online - Online Cellular Systems Modelling . Metabolic Pathways
. Signaling Pathways
Details
Free
SBML
DBTGR - DataBase of Tunicate Gene Regulation . Transcription Factors / Gene Regulatory NetworksDetails
Free
AffinDB - Affinity database for protein-ligand complexes . Protein-Compound InteractionsDetails
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 NetworksDetails
Free
SCOPPI - Structural classification of protein–protein interfaces . Protein-Protein InteractionsDetails
Free
iMOTdb - Interacting motifs in proteins database . Protein-Protein InteractionsDetails
Free
PINT - Protein–protein Interactions Thermodynamic Database . Protein-Protein InteractionsDetails
Free
NPInter - Noncoding RNAs and protein related biomacromolecules interaction databaseDetails
Free
miRBase - microRNA Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
MeRNA - Metals in RNADetailsUnavailable
Argonaute - Gene regulation by mammalian micro-RNAs . Transcription Factors / Gene Regulatory NetworksDetails
Free
MPromDb - Mammalian Promoter Database . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
HTPSELEX - HTPSELEX . Transcription Factors / Gene Regulatory NetworksDetails
Free
HemoPDB - Hematopoiesis Promoter Database . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
cisRED - Cis-regulatory element database . Transcription Factors / Gene Regulatory NetworksDetails
Free
ABS - Annotated regulatory Binding Sites . Transcription Factors / Gene Regulatory NetworksDetails
Free
CA1Neuron - Pathways of the hippocampal CA1 neuron . Protein-Protein Interactions
. Signaling Pathways
DetailsUnavailable
ERGO - ERGO Genome Analysis and Discovery System . Metabolic PathwaysDetailsLicense
Drastic - Database Resource for Analysis of Signal Transduction In Cells . Pathway DiagramsDetails
Free
DrugBank - DrugBank . Protein-Compound InteractionsDetails
Free
Ulysses - Projection of Protein Networks across Species . Protein-Protein InteractionsDetailsUnavailable
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
DetailsUnavailable
HCNet - Heart and Calcium Functional Network DatabaseDetailsUnavailable
SABIO-RK - SABIO-Reaction Kinetics Database . Metabolic PathwaysDetails
Free
BioPAX
SBML
RiceCyc - The rice metabolic pathway database . Metabolic PathwaysDetails
Free
PathFinder - Cell Signaling Pathways . Pathway DiagramsDetailsUnavailable
Pathway Slides - Cell Signaling Pathway Slides & Charts . Pathway DiagramsDetailsUnavailable
MiMI - Michigan Molecular Interactions . Protein-Protein Interactions
. Pathway Diagrams
Details
Free
PSI-MI
ECRbase - Evolutionary conserved region database . Transcription Factors / Gene Regulatory NetworksDetails
Free
UniHI - Unified Human Interactome . Protein-Protein InteractionsDetails
Free
PSP - Polygenic signaling pathways . Protein Sequence FocusedDetails
Free
MetNetDB - Metabolic Network Exchange . Metabolic PathwaysDetails
Free
PepBank - PepBank Peptide Database . Protein-Protein InteractionsDetails
Free
SIGMA-ALDRICH - Cell Signalling Pathway Slides & Charts . Signaling Pathways
. Pathway Diagrams
. Protein-Compound Interactions
DetailsUnavailable
WikiPathways - WikiPathways . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
BioPAX
gpDB - A Database of G-Proteins and their Interaction with GPCRs . Protein-Protein InteractionsDetails
Free
DOMINO - Domain Peptide Interactions Database . Protein-Protein InteractionsDetails
Free
CellCircuits - CellCircuits . Protein-Protein InteractionsDetails
Free
AthaMap - AthaMap . Transcription Factors / Gene Regulatory NetworksDetails
Free
PROTCOM - Database of Protein Complexes . Protein-Protein InteractionsDetailsUnavailable
SYSTOMONAS - SYSTems biology of pseudOMONAS . Metabolic Pathways
. Transcription Factors / Gene Regulatory Networks
Details
Free
HMDB - Human Metabolome Database . Metabolic PathwaysDetails
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 InteractionsDetailsUnavailable
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 InteractionsDetails
Free
CoryneRegNet - Database of Corynebacterial Transcription Factors and Regulatory Networks . Transcription Factors / Gene Regulatory NetworksDetails
Free
PhosphoPOINT - PhosphoPOINT . Protein-Protein InteractionsDetails
Free
GLIDA - GPCR-Ligand Database . Protein-Compound InteractionsDetails
Free
Binding MOAD - Binding Mother of all Databases . Protein-Compound InteractionsDetails
Free
PDBbind - PDBbind . Protein-Compound InteractionsDetailsAcademic
HDBase - Huntington's Disease Base . Protein-Protein InteractionsDetails
Free
P.R.I.S.M. - Protein Interactions by Structural Matching . Protein-Protein InteractionsDetails
Free
InterPare - The Protein Interfaceome Database . Protein-Protein InteractionsDetailsUnavailable
PlantCARE - Plant Cis-Acing Regulatory Elements . Transcription Factors / Gene Regulatory NetworksDetailsAcademic
AGRIS - Arabidopsis Gene Regulatory Information Server . Transcription Factors / Gene Regulatory NetworksDetails
Free
Athena - Athena . Transcription Factors / Gene Regulatory NetworksDetails
Free
DIMA - Domain Interaction Map . Protein-Protein InteractionsDetails
Free
PRIME - Protein interaction and molecular information database . Protein-Protein InteractionsDetailsUnavailable
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 NetworksDetails
Free
SGD Pathway Tools - Saccharomyces Genome Database Pathway Tools . Metabolic PathwaysDetails
Free
BioPAX
RGD - Rat Genome Database pathway resource . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
PlantCyc - Plant enzymes and biochemical pathways database . Metabolic PathwaysDetails
Free
BioPAX
MouseCyc - Mouse Pathway Database . Metabolic PathwaysDetails
Free
BioPAX
ITFP - Intergrated Transcription Factor Platform . Transcription Factors / Gene Regulatory NetworksDetails
Free
GO - Gene Ontology . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
Details
Free
MPIDB - Microbial Protein Interaction Database . Protein-Protein InteractionsDetails
Free
AraCyc - Arabidopsis enzymes and biochemical pathways database . Metabolic PathwaysDetails
Free
CPDB - ConsensusPathDB . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
DetailsAcademic
PSI-MI
PDTD - Potential Drug Target Database . Protein-Compound InteractionsDetails
Free
HuPI - database of the Human Proteotheque Initiative . Protein-Protein InteractionsDetails
Free
Interactome - Krogan Lab Interactome Database . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
PTM-Switchboard - Post-Translational Modification-Switchboard . Transcription Factors / Gene Regulatory NetworksDetails
Free
UniPROBE - Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation . Protein-Compound InteractionsDetails
Free
miRecords - miRecords . Transcription Factors / Gene Regulatory NetworksDetails
Free
sRNAMap - Small noncoding RNA Map . Protein-Compound InteractionsDetails
Free
TarBase - TarBase . Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
Details
Free
SuperSite - SuperSite . Protein-Compound InteractionsDetails
Free
PIG - Host Pathogen Interactions . Protein-Protein InteractionsDetails
Free
PiSITE - Database of Protein Interaction SITEs . Protein-Protein InteractionsDetails
Free
RsiteDB - RNA binding sites data base . Protein-Compound InteractionsDetails
Free
EciD - E. coli Interaction Database . Protein-Protein InteractionsDetailsUnavailable
PIPs - Human Protein-Protein Interaction Prediction . Protein-Protein InteractionsDetails
Free
VirHostNet - Virus-Host Network . Protein-Protein Interactions
. Pathway Diagrams
Details
Free
PSI-MI
ExPASy Biochemical Pathways - ExPASy - Roche Applied Science Biochemical Pathways . Metabolic PathwaysDetails
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 NetworksDetails
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 InteractionsDetails
Free
iRefWeb - Interaction Reference Index Web Interface . Protein-Protein InteractionsDetails
Free
PSI-MI
iRefIndex - Interaction Reference Index . Protein-Protein InteractionsDetails
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 InteractionsDetails
Free
PSI-MI
RKD - Rice Kinase Database . Protein-Protein InteractionsDetails
Free
BIPA - Biological Interaction database for Protein-nucleic Acid . Protein-Compound InteractionsDetails
Free
HDR - Homeodomain Resource Database . Protein Sequence FocusedDetails
Free
MycoRegNet - Mycobacterial transcription factors and regulatory networks . Transcription Factors / Gene Regulatory NetworksDetailsUnavailable
ADAN - Prediction of protein-protein interaction of modular domains . Protein-Protein InteractionsDetailsUnavailable
Rhea - Reaction databaseDetails
Free
BioPAX
SMPDB - Small Molecule Pathway Database . Metabolic Pathways
. Signaling Pathways
Details
Free
PepX - Peptide compleXes . Protein-Compound InteractionsDetailsUnavailable
STITCH - Chemical-Protein Interactions . Protein-Compound InteractionsDetails
Free
HAPPI - Human Annotated and Predicted Protein Interaction Database . Protein-Protein InteractionsDetails
Free
PSI-MI
NetPath - NetPath . Signaling PathwaysDetails
Free
PSI-MI
BioPAX
SBML
HumanCyc - Encyclopedia of Homo sapiens genes and metabolism . Metabolic Pathways
. Pathway Diagrams
DetailsAcademic
BioPAX
SBML
SPIKE - Signaling Pathway Integrated Knowledge Engine . Signaling Pathways
. Pathway Diagrams
DetailsAcademic
BioPAX
APID - Agile Protein Interaction DataAnalyzer . Protein-Protein InteractionsDetails
Free
MIPS-MPPI - MIPS Mammalian Protein-Protein Interaction Database . Protein-Protein InteractionsDetails
Free
PSI-MI
SignaLink 2 - SignaLink 2: a multi-layered signaling pathway resource . Signaling Pathways
. Pathway Diagrams
DetailsAcademic
PSI-MI
BioPAX
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 InteractionsDetails
Free
PSI-MI
GWIDD - Genome-WIde protein Docking Database . Protein-Protein InteractionsDetails
Free
HRTBLDb - Hormone Receptor Target Binding Loci Database . Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
Details
Free
SPLINTER - Structural Protein-Ligand Interactome . Protein-Compound InteractionsDetails
Free
T3DB - Toxin and Toxin-Target Database . Protein-Compound InteractionsDetails
Free
NCBI BioSystems - NCBI BioSystems . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
. Protein Sequence Focused
Details
Free
MetExplore - . Metabolic PathwaysDetails
Free
SBML
BiGG Knowledgebase - . Metabolic PathwaysDetailsAcademic
SBML
AtPID - Arabidopsis thaliana Protein Interactome Database . Protein-Protein InteractionsDetails
Free
MetaCrop - MetaCrop . Metabolic PathwaysDetails
Free
SBML
CORNET - CORrelation NETworks . Protein-Protein InteractionsDetails
Free
PathoPlant - . Signaling PathwaysDetails
Free
GeneMANIA - GeneMANIA . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
. Transcription Factors / Gene Regulatory Networks
. Genetic Interaction Networks
Details
Free
iPAVS - Integrated Pathway Resources, Analysis and Visualization System . Metabolic Pathways
. Signaling Pathways
DetailsAcademic
BioPAX
SBML
HTRIdb - Human Transcriptional Regulation Interaction Database . Protein-Protein Interactions
. Transcription Factors / Gene Regulatory Networks
Details
Free
ChEMBLdb - ChEMBL Database . Protein-Compound InteractionsDetails
Free
Ontocancro - Ontocancro . Signaling PathwaysDetails
Free
BioPAX
HINT-KB - Human INTeractome Knowledge Base . Protein-Protein InteractionsDetails
Free
AURA - Atlas of UTR Regulatory Activity . Transcription Factors / Gene Regulatory NetworksDetails
Free
MATADOR - Manually Annotated Targets and Drugs Online Resource . Protein-Compound InteractionsDetailsAcademic
SuperTarget - SuperTarget . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Protein-Compound Interactions
Details
Free
TDR Targets Database - The Tropical Disease Research Targets Database . Metabolic Pathways
. Protein-Compound Interactions
Details
Free
IUPHAR-DB - The International Union of Basic and Clinical Pharmacology Database . Protein-Compound InteractionsDetails
Free
Guide to Pharmacology - Guide to Pharmacology . Protein-Compound InteractionsDetails
Free
PAIR - The Predicted Arabidopsis Interactome Resource . Protein-Protein InteractionsDetails
Free
PSI-MI
HitPredict - HitPredict . Protein-Protein InteractionsDetails
Free
PINA - Protein Interaction Network Analysis . Protein-Protein InteractionsDetails
Free
MetaDrug - MetaDrug . Protein-Compound InteractionsDetailsLicense
BioPAX
SBML
PSICQUIC - Proteomics Standards Initiative Common QUery InterfaCe . Protein-Protein Interactions
. Protein-Compound Interactions
. Genetic Interaction Networks
Details
Free
PSI-MI
JAIL - JAIL . Protein-Protein InteractionsDetails
Free
MACPAK - Simulatable Macrophage Pathway Knowledgebase . Signaling PathwaysDetails
Free
IBIS - Inferred Biomolecular Interactions Server . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
SuperCYP - SuperCYP, Cytochrome P450 Database . Protein-Compound InteractionsDetails
Free
GeneOrienteer - Gene Orienteer . Genetic Interaction NetworksDetails
Free
PDBeMotif - Protein Data Bank in Europe, Motifs and Sites . Protein-Protein InteractionsDetails
Free
CREDO - CREDO: A Structural Interactomics Database For Drug Discovery . Protein-Compound InteractionsDetails
Free
BIANA - Biologic Interaction and Network Analysis . Protein-Protein InteractionsDetails
Free
CID - CISBAN Cross-Species Interactome Database . Genetic Interaction NetworksDetails
Free
MnM - Minimotif Miner . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
GeneTex - GeneTex . Pathway DiagramsDetails
Free
GeneGlobe - GeneGlobe . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
ChemProt - ChemProt . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
Bacteriome.org - Bacterial Protein Interaction Database for Escherichia Coli . Protein-Protein InteractionsDetails
Free
sc-PDB - An Annotated Database of Druggable Binding Sites from the Protein DataBank . Protein-Compound InteractionsDetails
Free
BISC - BInary SubComplex Database . Protein-Protein InteractionsDetails
Free
CutDB - CutDB: Proteolytic Event Database . Protein-Protein InteractionsDetails
Free
DOMINE - Database of Protein Domain Interactions . Protein-Protein InteractionsDetails
Free
DRYGIN - Data Repository of Yeast Genetic INteractions . Genetic Interaction NetworksDetails
Free
FunCoup - Networks of Functional Coupling . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
HotRegion - A Database of Cooperative Hotspots . Protein-Protein InteractionsDetails
Free
HotSprint - Database of Computational Hot Spots of Protein Interfaces . Protein-Protein InteractionsDetails
Free
InterEvol - InterEvol . Protein-Protein InteractionsDetails
Free
PepCyber - PepCyber: P~Pep . Protein-Protein InteractionsDetailsUnavailable
PSI-MI
prePPI - prePPI . Protein-Protein InteractionsDetails
Free
ProtCID - PROTein Common Interfaces Database . Protein-Protein InteractionsDetails
Free
PTMcode - PTMcode . Protein-Protein InteractionsDetails
Free
SynSysNet - Synaptic Proteins Database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
. Protein-Compound Interactions
Details
Free
TissueNet - The Database of Human Tissue Protein-Protein Interactions . Protein-Protein InteractionsDetails
Free
VirusMINT - VirusMINT . Protein-Protein InteractionsDetails
Free
PSI-MI
Bionemo - Biodegradation Network Molecular Biology Database . Metabolic PathwaysDetails
Free
ECMDB - E. Coli Metabolome Database . Metabolic PathwaysDetails
Free
hiPathDB - human integrated Pathway DB with facile visualization . Metabolic Pathways
. Signaling Pathways
Details
Free
YMDB - The Yeast Metabolome Database . Metabolic PathwaysDetails
Free
NetworKIN - NetworKIN . Protein-Protein InteractionsDetails
Free
RegPhos - Regulatory Network in Protein Phosphorylation . Protein-Protein Interactions
. Signaling Pathways
Details
Free
2P2Idb - The Protein-Protein Interaction Inhibition Database . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
3D-Interologs - 3D-Interologs . Protein-Protein InteractionsDetails
Free
AnimalTFDB - Animal Transcription Factor Database . Protein-Protein Interactions
. Transcription Factors / Gene Regulatory Networks
Details
Free
BioLiP - Ligand-Protein Binding Database . Protein-Compound InteractionsDetails
Free
CancerResource - CancerResource . Protein-Compound InteractionsDetails
Free
RCSB PDB - The Research Collaboratory for Structural Bioinformatics Protein Data Bank . Protein-Compound InteractionsDetails
Free
EndoNet - EndoNet . Signaling PathwaysDetails
Free
KUPS - The University of Kansas Proteomics Service . Protein-Protein InteractionsDetails
Free
LigASite - Ligand Attachment Site . Protein-Compound InteractionsDetails
Free
MiST2 - Microbial Signal Transduction Database 2 . Protein-Protein Interactions
. Signaling Pathways
Details
Free
MPID-T2 - MHC-Peptide Interaction Database-TR . Protein-Protein InteractionsDetails
Free
PCRPi-DB - Presaging Critical Residues in Protein interfaces-DataBase . Protein-Protein InteractionsDetails
Free
Predictive Networks - Predictive Networks . Genetic Interaction NetworksDetails
Free
PRRDB - Pattern Recognition Receptor Database . Signaling Pathways
. Protein-Compound Interactions
Details
Free
CCDB - The Cell Cycle Database . Signaling PathwaysDetails
Free
SBML
TRIP - Mammalian Transient Receptor Potential Channel-Interacting Protein . Protein-Protein InteractionsDetails
Free
KaPPA-View - Kazusa Plant Pathway Viewer . Metabolic Pathways
. Pathway Diagrams
Details
Free
LAMP - (Liverpool) Library of Apicomplexan Metabolic Pathways . Metabolic Pathways
. Pathway Diagrams
Details
Free
MMMDB - Mouse Multiple tissue Metabolome DataBase . Metabolic PathwaysDetails
Free
MODOMICS - Modomics: a database of RNA modification pathways . Metabolic PathwaysDetails
Free
UniPathway - UniPathway: a resource for the exploration of metabolic pathways . Metabolic PathwaysDetails
Free
PMAP - The Proteolysis Map . Metabolic Pathways
. Signaling Pathways
Details
Free
WholeCellKB - WholeCellKB: Mycoplasma Genitalium Database . Metabolic PathwaysDetails
Free
REPAIRtoire - REPAIRtoire: a database of DNA repair pathways . Signaling PathwaysDetails
Free
IMEx - The International Molecular Exchange Consortium . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
PSI-MI
DOMMINO - Database of MacroMolecular Interactions . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
Human-gpDB - A database of human GPCRs, G-proteins, Effectors and their interactions . Protein-Protein InteractionsDetails
Free
PhosphoGRID - PhosphoGRID . Protein-Protein InteractionsDetails
Free
WormBase - Worm Base . Protein-Protein Interactions
. Transcription Factors / Gene Regulatory Networks
. Genetic Interaction Networks
Details
Free
GermOnline - GermOnline . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
Pigment Cell Gene Resource - Pigment Cell Gene Resource . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
PROFESS - Protein Function, Evolution, Structure and Sequence Database . Protein-Protein Interactions
. Protein Sequence Focused
Details
Free
NetSlim - NetSlim . Signaling Pathways
. Pathway Diagrams
Details
Free
PSI-MI
BioPAX
SBML
TAIR - The Arabidopsis Information Resource . Metabolic PathwaysDetails
Free
SGN - Sol Genomics Network . Metabolic Pathways
. Pathway Diagrams
Details
Free
GRAMENE - Plant Metabolic Pathways . Metabolic Pathways
. Pathway Diagrams
Details
Free
Dr. PIAS - Druggable Protein-protein Interaction Assessment System . Protein-Protein InteractionsDetails
Free
RiceSRTFDB - The Rice Stress-Responsive Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
PMP - The Protein Model Portal . Protein Sequence FocusedDetails
Free
YY1TargetDB - Yin Yang 1 Target Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
CHD@ZJU - Coronary Heart Disease @ZJU Database . Protein-Protein Interactions
. Signaling Pathways
. Pathway Diagrams
Details
Free
TetraFGD - Tetrahymena Functional Genomics Database . Transcription Factors / Gene Regulatory Networks
. Genetic Interaction Networks
Details
Free
DeathDomain - Death Domain Database . Protein-Protein InteractionsDetailsUnavailable
ModBase - ModBase . Protein-Protein Interactions
. Protein Sequence Focused
Details
Free
Negatome - The Negatome Database . Protein-Protein InteractionsDetails
Free
PCDB - Protein Conformational Database . Protein-Protein InteractionsDetails
Free
DASMI - Distributed Annotation System for Molecular Interactions . Protein-Protein InteractionsDetails
Free
PeroxisomeDB - Peroxisome Database . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
PoSSuM - Pocket Similarity Search using Multi-Sketches . Protein-Compound InteractionsDetails
Free
ProtChemSI - ProtChemSI: the database of protein-chemical structural interactions . Protein-Compound InteractionsDetails
Free
TcoF-DB - Dragon Database of Transcription co-factors and transcription factor interacting proteins . Transcription Factors / Gene Regulatory NetworksDetails
Free
Yeast KID - Yeast Kinase Interaction Database . Protein-Protein InteractionsDetails
Free
drug2gene - drug2gene . Protein-Compound InteractionsDetails
Free
PROMISCUOUS - PROMISCUOUS . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Protein-Compound Interactions
Details
Free
DAnCER - Disease Annotated Chromatin Epigenetics Resource . Protein-Protein InteractionsDetails
Free
ScerTF - ScerTF . Transcription Factors / Gene Regulatory NetworksDetails
Free
iProClass - iProClass . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
Cyclonet - Cyclonet . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
MedicCyc 2.0 - Medicago truncatula Pathway Database . Metabolic Pathways
. Pathway Diagrams
Details
Free
BioPAX
FlyBase - FlyBase: a database of Drosophila Genes & Genomes . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
PDBsum - PDBsum: pictorial database of 3D structures in the Protein Data Bank . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
MaizeCyc - MaizeCyc: metabolic pathways in maize . Metabolic Pathways
. Pathway Diagrams
Details
Free
BioPAX
H-InvDB - H-InvDB: Annotated Human Gene Database . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
Biozon - Biozon . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
SYNDB - Synapse Database . Protein-Protein Interactions
. Metabolic Pathways
. Protein-Compound Interactions
Details
Free
RegTransBase - RegTransBase . Transcription Factors / Gene Regulatory NetworksDetails
Free
NPIDB - Nucleic Acid-Protein Interaction DatabaseDetails
Free
IntPath - Integrated Pathway Gene Relationship Database . Protein-Protein Interactions
. Metabolic Pathways
. Pathway Diagrams
Details
Free
BsubCyc - BsubCyc . Metabolic Pathways
. Pathway Diagrams
Details
Free
BioPAX
NCG - Network of Cancer Genes . Protein-Protein InteractionsDetails
Free
PRIMOS - Protein Interaction and Molecule Search database . Protein-Protein InteractionsDetails
Free
XooNET - Integrated Protein-Protein Interaction database of Xanthomonas oryzae pathovar oryzae KACC1031 . Protein-Protein InteractionsDetails
Free
SPIDer - Saccharomyces Protein-protein Interaction Database . Protein-Protein InteractionsDetails
Free
InterPreTS - Interaction Prediction through Tertiary Structure . Protein-Protein InteractionsDetailsAcademic
SPPS - Sequence-based Protein Partner Search . Protein-Protein InteractionsDetails
Free
HINT - High-quality Interactomes . Protein-Protein InteractionsDetails
Free
INstruct - a database of 3D protein interactome networks with structural resolution . Protein-Protein InteractionsDetails
Free
PRD - Protein-RNA Interaction DatabaseDetails
Free
PSI-MI
SCOWLP - structural classification of protein binding reasons for atomic comparative analysis of protein interactions . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
MPI-LIT - the microbial protein interaction database . Protein-Protein InteractionsDetails
Free
P2TF - Predicted Prokaryotic Transcription Factors . Transcription Factors / Gene Regulatory NetworksDetails
Free
DAPID - Domain Annotated Protein-protein Interaction Database . Protein-Protein InteractionsDetails
Free
InterMitoBase - InterMitoBase . Protein-Protein InteractionsDetails
Free
HPD - Human Pathway Database . Metabolic Pathways
. Signaling Pathways
Details
Free
IPAD - the Integrated Pathway Analysis Database for Systematic Enrichment Analysis . Metabolic PathwaysDetails
Free
SUBA3 - The SUBcellular localization database for Arabidopsis proteins . Protein-Protein InteractionsDetails
Free
PPIRA - Protein-Protein Interactions between Ralstonia solanacearum and Arabidopsis thaliana . Protein-Protein InteractionsDetails
Free
Snap - a Single Nucleotide Polymorphism Annotation Platform . Protein-Protein Interactions
. Metabolic Pathways
. Genetic Interaction Networks
Details
Free
COXPRESdb - Coexpressed Gene Database . Protein-Protein InteractionsDetails
Free
DBD - DNA-Binding Domain: Transcription Factor Predictor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
PlantTFDB - Plant Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
DRTF - Database of Rice Transcription Factors . Transcription Factors / Gene Regulatory NetworksDetails
Free
rSNP Guide - rSNP Guide . Transcription Factors / Gene Regulatory NetworksDetails
Free
TrSDB - A Proteome Database of Transcription Factors . Transcription Factors / Gene Regulatory NetworksDetails
Free
LIPID MAPS - LIPID Metabolites and Pathways Strategy . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
mips Mpact - Protein Interaction and Complex Database . Protein-Protein InteractionsDetailsUnavailable
PSI-MI
Gene3D - Gene3D . Protein-Protein InteractionsDetails
Free
MMDB - Molecular Modeling Database . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
FLIGHT - FLIGHT . Protein-Protein Interactions
. Genetic Interaction Networks
Details
Free
FlyMine - FlyMine . Metabolic Pathways
. Signaling Pathways
. Genetic Interaction Networks
Details
Free
FlyReactome - FlyReactome: a curated knowledgebase of drosophila melanogaster pathways . Metabolic Pathways
. Signaling Pathways
Details
Free
BioPAX
SBML
FlyTF - The Drosophila Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
Nematode.net - Nematode.net . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
PlasmoDB - PlasmoDB . Metabolic Pathways
. Pathway Diagrams
Details
Free
SIMAP - The Similarity Matrix of Proteins . Protein Sequence FocusedDetails
Free
ATDB - Animal Toxin Database . Protein-Protein Interactions
. Protein-Compound Interactions
Details
Free
DB-PABP - Database of Polyanion Binding Proteins . Protein-Compound InteractionsDetails
Free
DATF - Database of Arabidopsis Transcription Factors . Transcription Factors / Gene Regulatory NetworksDetails
Free
MitoProteome - MitoProteome Database . Metabolic Pathways
. Signaling Pathways
. Protein Sequence Focused
Details
Free
GDR Cyc Pathways - Genome Database for Rosaceae Cyc Pathways . Metabolic Pathways
. Signaling Pathways
. Pathway Diagrams
Details
Free
BioPAX
PAZAR - A Public Database of Transcription Factor and Regulatory Sequence Annotation . Transcription Factors / Gene Regulatory NetworksDetails
Free
AS-ALPS - Alternative Splicing - induced ALteration of Protein Structure . Protein-Protein InteractionsDetails
Free
metaTIGER - metaTIGER: metabolic gene evolution resource . Metabolic Pathways
. Pathway Diagrams
Details
Free
Human Proteinpedia - Human Proteinpedia . Protein-Protein InteractionsDetails
Free
RAPID - Resource of Asian Immunodeficiency Diseases . Protein-Protein InteractionsDetails
Free
AHD2.0 - Arabidopsis Hormone Database 2.0 . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
RiceGeneThresher - RiceGeneThresher: bioinformatics tool site for rice genes discovery . Protein-Protein Interactions
. Metabolic Pathways
Details
Free
RegPrecise - RegPrecise: Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes . Transcription Factors / Gene Regulatory NetworksDetails
Free
phiSITE - phiSITE: Database of Gene Regulation in Bacteriophages . Transcription Factors / Gene Regulatory NetworksDetails
Free
GLAMM - Genome-Linked Application for Metabolic Maps . Metabolic Pathways
. Pathway Diagrams
Details
Free
PlnTFDB - Plant Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
FlyFactorSurvey - FlyFactorSurvey: Database of Drosophila TF DNA-Binding Specifities . Transcription Factors / Gene Regulatory NetworksDetails
Free
PRIDB - Protein-RNA Interface DatabaseDetails
Free
YPA - Yeast Promoter Atlas . Protein-Protein Interactions
. Transcription Factors / Gene Regulatory Networks
Details
Free
ASD - Allosteric Database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
Details
Free
CADgene - Coronary Artery Disease Gene Database . Protein-Protein Interactions
. Metabolic Pathways
. Genetic Interaction Networks
Details
Free
Pocketome - Pocketome . Protein-Compound InteractionsDetails
Free
DNAtraffic - DNAtraffic Database . Signaling PathwaysDetails
Free
SubtiPathways - SubtiPathways . Metabolic PathwaysDetails
Free
BiologicalNetworks - BiologicalNetworks . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Genetic Interaction Networks
Details
Free
FMM - From Metabolite to Metabolite . Metabolic PathwaysDetails
Free
PI2PE - Protein Interface/Interior Prediction Engine . Protein-Protein InteractionsDetails
Free
SynechoNET - SynechoNet: Integrated Protein-Protein Interaction Database of Synechocystis sp. PCC 6803 . Protein-Protein InteractionsDetails
Free
T2D-Db - T2D-Db: An Integrated Data Resource on Type 2 Diabetes . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
Details
Free
Wiki-Pi - Wiki-Pi: a wiki resource centred on human protein-protein interactions . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
Details
Free
CCSB Interactome Database - Center for Cancer Systems Biology Interactome Database . Protein-Protein InteractionsDetails
Free
GenAge - GenAge: The Ageing Gene Database . Protein-Protein InteractionsDetails
Free
MitoP2 - Mitochondrial Proteome . Protein-Protein InteractionsDetails
Free
PICCOLO - PICCOLO . Protein-Protein InteractionsDetails
Free
PRIN - Predicted Rice Interactome Database . Protein-Protein InteractionsDetails
Free
AraNet - AraNet: Probabilistic Functional Gene Network of Arabidopsis Thaliana . Genetic Interaction NetworksDetails
Free
HomoMINT - Human Molecular Interaction Database . Protein-Protein InteractionsDetails
Free
PSI-MI
AtPIN - Arabidopsis thaliana Protein Interactome Network . Protein-Protein InteractionsDetails
Free
DIPOS - Database of Interacting Proteins in Oryza Sativa . Protein-Protein InteractionsDetails
Free
HCVpro - Hepatitus C Virus Protein Interaction Database . Protein-Protein InteractionsDetailsAcademic
HIPPIE - Human Integrated Protein-Protein Interaction rEference . Protein-Protein InteractionsDetails
Free
HPIDB - Host-Pathogen Interaction Database . Protein-Protein InteractionsDetails
Free
PSI-MI
MitoInteractome - Mitochondrial Protein Interactome Database . Protein-Protein InteractionsDetails
Free
PSI-MI
MPID - Magnaporthe grisea Protein-protein Interaction Database . Protein-Protein InteractionsDetails
Free
MppDB - Mouse Protein-Protein Interaction Database . Protein-Protein InteractionsDetails
Free
NCPI - Neurospora Crassa Protein Interactome Database . Protein-Protein InteractionsDetails
Free
PutidaNET - PutidaNET . Protein-Protein InteractionsDetails
Free
Struct2Net - Structure-based Computational Predictions of Protein-Protein Interactions . Protein-Protein InteractionsDetails
Free
STIFDB - Stress Responsive Transcription Factor Database . Transcription Factors / Gene Regulatory NetworksDetails
Free
BESC BeoCyc - BioEnergy Science Center BeoCyc . Metabolic PathwaysDetails
Free
BioPAX
CathaCyc - CathaCyc: Metabolic Pathway Database of Catharanthus roseus . Metabolic PathwaysDetails
Free
BioPAX
PAGED - Pathway and Gene Enrichment Database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Transcription Factors / Gene Regulatory Networks
Details
Free
IMID - Integrated Molecular Interaction Database . Protein-Protein Interactions
. Metabolic Pathways
. Signaling Pathways
. Protein-Compound Interactions
Details
Free
IRView - IRView . Protein-Protein InteractionsDetails
Free
PSI-MI
DroPNet - Drosophila Protein Network . Protein-Protein InteractionsDetails
Free
AraPath - AraPath: a knowledgebase for pathway analysis in Arabidopsis . Metabolic Pathways
. Signaling Pathways
DetailsAcademic
AtIPD - Arabidopsis thaliana Isoprenoid Pathway Database . Metabolic Pathways
. Pathway Diagrams
Details
Free
ANAP - Arabidopsis Network Analysis Pipeline . Protein-Protein InteractionsDetails
Free
IMP - Integrative Multi-species Prediction . Metabolic Pathways
. Genetic Interaction Networks
Details
Free
FPPI - Fussarium graminearum Protein-Protein Interaction Database . Protein-Protein InteractionsDetails
Free
hPDI - Human Protein-DNA Interactome . Transcription Factors / Gene Regulatory Networks
. Protein-Compound Interactions
Details
Free
RNApathwaysDB - RNA Pathways Database: a database of RNA maturation and decay . Metabolic PathwaysDetails
Free


"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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