Protein Sequence Databases
- SWISS-PROT - Annotated protein sequence database
- NCBI/EMBL - Entrez protein search and retrieval system
- PIR - Protein Information Resource database
Protein-Protein Interaction Databases
- BIND - Biomolecular INteraction Network Database
- BioGRID - The Biological General Repository for Interaction Datasets
- DIP - Database of Interacting Proteins
- HPRD - Human Protein Reference Database
-
IntAct - Open source database system and analysis tools for protein interaction data.
- MINT - Molecular INTeraction database
- MPact - The MIPS Mammalian Protein-Protein Interaction Database
- PathGuide - A listing of all online sources of PPI data
- STRING - Protein networks based on experimental data and predictions at EMBL
- PSICQUIC Viewer - An application that uses PSICQUIC behind the scenes, displaying search results from several molecular interaction databases.
Other databases
- LUMIER - LUminescence-based Mammalian IntERactome
Data Exchange Formats
- PSI-MI - Proteomics
Standards Initiative Molecular Interaction XML Format
- BioPAX - Biological Pathways Exchange
- GML - Graph Modeling Language
Visualization Tools
- NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto
- Cytoscape - A software environment for integrated models of biomolecular interaction networks
- Osprey - A network visualization system
- Pajek - A program for large network analysis.
Literature Search
- PubMed - Literature retrieval system from NCBI/NLM
- IMEx - The International Molecular Exchange Consortium