A wealth of in silico tools is available for protein motif discovery and 
structural analysis. The aim of this chapter is to collect some of the most 
common and useful tools and to guide the biologist in their use. A detailed 
explanation is provided for the use of Distill, a suite of web servers for the 
prediction of protein structural features and the prediction of full-atom 3D 
models from a protein sequence. Besides this, we also provide pointers to many 
other tools available for motif discovery and secondary and tertiary structure 
prediction from a primary amino acid sequence. The prediction of protein 
intrinsic disorder and the prediction of functional sites and SLiMs are also 
briefly discussed. Given that user queries vary greatly in size, scope and 
character, the trade-offs in speed, accuracy and scale need to be considered 
when choosing which methods to adopt.