  This chapter deals with approaches for protein three-dimensional structure
prediction, starting out from a single input sequence with unknown struc- ture,
the 'query' or 'target' sequence. Both template based and template free
modelling techniques are treated, and how resulting structural models may be
selected and refined. We give a concrete flowchart for how to de- cide which
modelling strategy is best suited in particular circumstances, and which steps
need to be taken in each strategy. Notably, the ability to locate a suitable
structural template by homology or fold recognition is crucial; without this
models will be of low quality at best. With a template avail- able, the quality
of the query-template alignment crucially determines the model quality. We also
discuss how other, courser, experimental data may be incorporated in the
modelling process to alleviate the problem of missing template structures.
Finally, we discuss measures to predict the quality of models generated.
