Continual advancements in computing power and sophistication, coupled with rapid increases in protein sequence and structural information, have made bioinformatic tools an invaluable resource for the molecular and structural biologists. With the degree of sequence information continuing to expand at an almost exponential rate, it is essential that scientists today have a basic understanding of how to utilise, manipulate, and analyse this information for the benefit of their own experiments. In the context of Toll-interleukin-1 receptor (TIR) domain containing proteins, we describe here a series of the more common and user-friendly bioinformatic tools available as internet-based resources. These will enable the identification and alignment of protein sequences, the identification of functional motifs, the characterisation of protein secondary structure, the identification of protein structural folds and distantly homologous proteins, and the validation of the structural geometry of modelled protein structures.