Large molecular datasets from genomic and proteomic studies present logistical problems of analysis, integration and ultimately usefulness, in part because of a shortage of suitable tools for their organization and maintenance. This problem was encountered when we began to investigate the molecular network of synapse proteins controlling neuronal plasticity and learning (Husi et al., 2000). Here, the N-methyl-D-aspartate receptor was part of a multiprotein complex (NRC) comprising 77 proteins, which themselves are part of the post synaptic density (PSD) that comprises over 700 proteins. We describe progress toward the construction of a Protein-Protein Interaction Database (PPID) comprising the NRC and PSD proteins and proteins known to interact with them. This database should serve several purposes including clustering and integration of datasets to facilitate the display and comprehensive analysis of biological systems including the synapse.