Modular protein domains are nature's solution for building versatile proteins from ready-made building blocks, but keeping track of how they've been shuffled is no easy task. Simple Modular Architecture Research Tool (SMART), written by Peer Bork's group at the European Molecular Biology Laboratory in Heidelberg, is a powerful tool for putting domains in context.

The simplest way to familiarize yourself with SMART's database of over 400 characterized domains is to click on an entry in the list. This categorizes the occurrence of each domain according to evolutionary distribution and cellular location, as well as including information on structure and function. You can also do sequence alignments.

More specific searches can be done on two levels: sequence or architecture. You can simply paste in a sequence or type in accession numbers from all the commonly used protein databases. If you already know what modular domains your protein of interest contains, you can use the architecture tool to search for proteins that contain the same combination of domains. You can also narrow your search down to a particular organism or group of organisms.

SMART can also represent groups of proteins as 'beads on a string' cartoons — an effective way to compare the architecture of a group of proteins. All the 'beads' in these cartoons are clickable, taking you through to that domain's page.

Data entry is a bit clumsy (for instance, the Boolean operators only work if you type them in upper case), but it's worth perservering; even if you don't have a specific query, half an hour spent playing with SMART will reveal nature's uncanny capacity to reuse the same module in many contexts.