Saccharomyces Genome Database
SGD™ is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
SGD publication(s)

Flybase
FlyBase is the primary database of genetic and genomic data for the insect family Drosophilidae.
Flybase publication(s)

Scansite
Scansite provides tools for proteome-wide prediction of cell signaling interactions using short sequence motifs
Scansite publication(s)

OrthoMCL
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.
OrthoMCL publication(s)

STRING
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein-protein interactions.
STRING publication(s)

KEGG
KEGG is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE).
KEGG publication(s)

Cytoscape
Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
Cytoscape publication(s)

ISB Phosphopep