| APID | Agile Protein Interactomes DataServer |
| BioGRID | Biological General Repository for Interaction Datasets |
| NPIDB | Database for the automated and interactive analysis of protein–DNA complexes |
| 3DID | Database of 3D interacting domains |
| GpDB | Database of GPCRs, G-proteins, Effectors and their interactions |
| DIP | Database of Interacting Proteins |
| PiSITE | Database of Protein interaction SITEs |
| iMOTdb | Database of Spatially Interacting Motifs in Proteins |
| CC+ | Database of coiled-coil structures |
| DOMMINO | Database of macromolecular interactions |
| BindingDB | Database of measured binding affinities for small, drug-like molecules |
| PIBASE | Database of structurally defined protein interfaces |
| MatrixDB | Database on interactions between extracellular proteins and polysaccharides |
| DynaSIN | Dynamic Structure Interaction Network |
| GPCRdb | G-protein coupled receptors (GPCRs) Database |
| GPS-Prot | Human protein-protein interactions (PPI). HIV-1 protein interactions. |
| InterEvol database for the analysis of co-evolution events at the interface of protein structures |
| IMEx | International Molecular Exchange Consortium |
| I2D | Interologous Interaction Database of known and predicted mammalian and eukaryotic protein-protein interactions |
| MIPS | Mammalian Protein-Protein Interaction Database |
| IntAct | Molecular Interaction Database |
| MINT | Molecular Interactions Database |
| ADAN | Prediction of protein-protein interAction of moDular domAiNs |
| STRING | Protein-Protein Interaction Networks |
| InterProSurf | Protein-Protein Interaction Server |
| Spiricoil | Proteins containing coiled coils in genomes |
| PDBe PISA | Proteins, Interfaces, Structures and Assemblies |
| HuRI | Reference map of the human binary protein interactome |
| PPI3D | Server for searching, analyzing and modeling protein interactions in the context of 3D structures |
| UniHI | Unified Human Interactome |
