Toll-like receptors (TLRs) play a central role in bridging the innate and adaptive immune responses. TLR signaling pathways are also implicated in serious autoimmune diseases such as endotoxic shock and thus are important therapeutic targets. Owing to the lack of TLR structural information, explanations for ligand-binding mechanisms have been difficult to provide. Computational modeling enables initial predictions of three-dimensional structures for the investigation of receptor-ligand interaction mechanisms. In order to understand the nature of the interactions of the TLR ECD with their...