DIP: the database of interacting proteins

Abstract

The Database of Interacting Proteins (DIP; http://dip.doe-mbi.ucla.edu) is a database that documents experimentally determined protein-protein interactions. This database is intended to provide the scientific community with a comprehensive and integrated tool for browsing and efficiently extracting information about protein interactions and interaction networks in biological processes. Beyond cataloging details of protein-protein interactions, the DIP is useful for understanding protein function and protein-protein relationships, studying the properties of networks of interacting proteins, benchmarking predictions of protein-protein interactions, and studying the evolution of protein-protein interactions.

Figure 1

The relational structure of the DIP. The protein information (left) is linked to the interaction table (center), which in turn is linked to the experiment table (right). An interaction is a unique entry but can be linked to many different experiments.

Figure 2

Diagram of 57 interacting proteins functioning in cell cycle and transcription control contained in the DIP database. Each open circle represents a protein; each line is an experimentally determined interaction. Cell division protein kinase 6 (Cdk6) bridges cell cycle control proteins with transcription related proteins by interacting with both cyclin dependent kinase inhibitor (Kip1) and E2F related transcription factor (DP1). The highlighted proteins are the following: Rb (retinoblastoma associated protein), Kip1 (cyclin dependent kinase inhibitor), TBP (TATA binding protein associated factor II), cyclin B1 (G2/mitotic specific cyclin B1), cdc25 (M phase inducer phosphatase 1), raf1 (proto-oncogene ser/thr protein kinase), ras (transforming protein p21/ras).