BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be drug-targets with small, drug-like molecules. It contains binding data for over 2 million protein-ligand complexes with experimental measurements including Ki, Kd, IC50, and EC50 values.

BRENDA is the main collection of enzyme functional data available to the scientific community.

CellChatDB is a manually curated database of literature-supported cell-cell communication interactions for CellChat, including ligand-receptor pairs, multi-subunit complexes and signaling cofactors across multiple species.

Cellinker is a literature-curated repository of ligand-receptor interactions involved in cell-cell communication, including protein ligands, metabolite ligands, receptors, enzymes and transporters.

CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions, designed to enable the analysis of cell-cell communication from single-cell transcriptomics data.

ChEBI is a manually curated database and ontology of small molecular entities. This inputs_v2 module emits searchable small-molecule entities with ontology hierarchy edges derived from the official OBO release.

ChEMBL is a manually curated chemical database of bioactive molecules with drug-like properties.

ChemOnt is the chemical taxonomy used by ClassyFire for hierarchical chemical classification of compounds.

ConnectomeDB is a comprehensive and ongoing project that provides ahigh-quality manually curated database of interacting ligand-receptorpairs for use in cell-cell communication analysis. First released in2015 (Ramilowski, et al.), and subsequently updated in 2020 (Hou, et al.)and 2025 (Liu, Maezono et al.), it aims to enhance the understanding ofcell-cell communication in humans and other mammals, supporting biologicaland medical research.

CORUM is a manually curated repository of experimentally characterized protein complexes from mammalian organisms. Each complex includes information about subunit composition, functional annotations, and literature references.

DrugCentral is an online drug information resource with active ingredients, chemical entities, pharmacologic action, indications, mechanism of action and drug-target interaction data.

FooDB is the world's largest and most comprehensive resource on food constituents, chemistry and biology. It provides information on both macronutrients and micronutrients, including compounds that give foods their taste, colour, texture and aroma.

The Gene Ontology provides controlled vocabulary terms for gene product function, process, and cellular location.

The IUPHAR/BPS Guide to PHARMACOLOGY is an expert-curated resource of ligand-activity-target relationships, providing quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. It covers G protein-coupled receptors, voltage-gated ion channels, ligand-gated ion channels, nuclear hormone receptors, catalytic receptors, enzymes, and transporters.

Human-GEM is a genome-scale metabolic model of human metabolism maintained by the SysBioChalmers group.

The Human Metabolome Database (HMDB) is a comprehensive database containing detailed information about small molecule metabolites found in the human body. It includes chemical, clinical, and biochemical/molecular biology data, with over 220,000 metabolite entries including both water-soluble and lipid-soluble metabolites.

The Human Phenotype Ontology (HPO) provides a standardized vocabulary for describing phenotypic abnormalities encountered in human disease. This module provides gene-phenotype associations linking genes to HPO terms.

ICELLNET is a transcriptomic framework with an expert-curated human ligand-receptor interaction database accounting for multi-subunit ligands and receptors.

A high-quality mouse genome-scale metabolic reconstruction, iMM1415(Mus Musculus, 1415 genes)

IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available in PSI-MITAB format. The database includes protein-protein, protein-small molecule and protein-nucleic acid interactions with detailed experimental evidence.

Biochemical reactions from KEGG REACTION, with exact KEGG compound participants parsed from reaction equations and enriched with EC, Rhea, KO, RCLASS, ChEBI, and PubChem identifiers.

The LIPID MAPS Structure Database (LMSD) is a comprehensive database of lipid structures, annotations, and cross-references. It contains over 47,000 unique lipid structures, classified according to a comprehensive lipid classification system. The database includes structure-based identifiers (InChI, InChIKey, SMILES), chemical properties (formula, exact mass), lipid classification (category, main class, sub class), and cross-references to other databases (ChEBI, PubChem, SwissLipids, HMDB).

MACdb is a comprehensive knowledgebase based totally on manual curation of cancer metabolic literature, providing high quality metabolite associations, online visualizing networks, and other effective tools for cancer or metabonomics researches.

MEBOCOST DB is a curated resource of metabolite-sensor interactions collected through computational text-mining and manual curation from PubMed abstracts and databases like HMDB, Recon2, and GPCRdb.

miRBase is the primary public repository and online resource for microRNA sequences and annotation. This inputs_v2 module emits precursor (MI#) and mature (MIMAT#) miRNAs as distinct entities joined by maturation relations.

The Mondo Disease Ontology harmonizes disease concepts across sources. This module provides the MONDO OBO ontology and gene-disease associations encoded as MONDO relationships to HGNC genes.

MRClinksDB is a curated database of metabolite–receptor interactions, covering ligand-receptor pairs with compound classification based on the ClassyFire taxonomy, receptor UniProt identifiers, and PubMed literature support.

NeuronChat is a manually curated resource of neural-specific intercellular molecular interactions, designed for inferring neuron-neuron communication from single-cell and spatial transcriptomics data.

NicheNet v2 ligand-receptor networks provide prior knowledge for modeling intercellular communication by linking sender-cell ligands to receiver-cell receptors and downstream target gene regulation.

OmniPath controlled vocabulary ontology export.

PFOCR (Pathway Figure OCR) extracts genes and chemicals from pathway figures in the biomedical literature. This module parses the current WikiPathways PFOCR GMT exports.

Phenol-Explorer is the first comprehensive database on polyphenol content in foods. It contains data on the content and composition of polyphenols and other bioactive compounds in foods, with detailed classification of both compounds and food sources.

The PSI-MI controlled vocabulary provides molecular interaction terms and metadata.

PTFI Discover is a comprehensive database of food composition and metabolomics data, providing detailed information on chemical compounds found in foods with statistical measurements across multiple samples.

RaMP-DB (Relational database of Metabolomic Pathways) is a multi-sourced integrated database with comprehensive annotations on biological pathways, structure/chemistry, disease and ontology annotations for genes, proteins, and metabolites.

Reactome is a free, open-source, curated and peer-reviewed pathway database.

Recon3D is a comprehensive human genome-scale metabolic reconstruction that accounts for three-dimensional molecular structures.

The main objective of RefMet is to provide a standardized reference nomenclature for both discrete metabolite structures and metabolite species identified by spectroscopic techniques in metabolomics experiments

Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest.

SIGNOR (SIGnaling Network Open Resource) is a comprehensive resource of causal relationships between biological entities with a focus on signaling pathways. It provides manually curated interactions with mechanistic details including protein-protein interactions, post-translational modifications, transcriptional regulation, and small molecule effects.

The SLC (Solute Carrier) series includes the “classical” transporter families (ion-coupled transporters, exchangers, passive transporters, etc.). It contains 65 SLC gene families with 458 different human transporter genes, thus representing a major portion of the human transporter-related genes.

STITCH is a database of known and predicted interactions between chemicals and proteins. Interactions include direct (physical) and indirect (functional) associations derived from genomic context, high-throughput experiments, conserved coexpression, and published literature.

SwissLipids is a curated resource providing a framework for the annotation of mass spectrometry data. It provides over 750,000 lipid structures with expert curation of lipid classes and nomenclature, hierarchical organization, cross-references to other databases (ChEBI, LIPID MAPS, HMDB), and integration with mass spectrometry tools. The database covers all major lipid categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids, saccharolipids, and polyketides.

The Transporter Classification Database (TCDB) provides a comprehensive classification system for membrane transport proteins based on both function and phylogeny. It assigns TC numbers to transporters and curates their substrates using CHEBI identifiers.

UniProt is a comprehensive resource for protein sequence and functional information. It provides high-quality, manually annotated protein data including function, structure, localization, interactions, disease associations, and cross-references to other databases.

WikiPathways is a community-curated pathway database. This inputs_v2 module parses the current RDF pathway export and emits pathway and directed interaction entities.