The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.
Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.