Homology models are useful to get a rough idea where the alpha carbons of key residues sit the folded protein. They can guide mutagenesis experiments, or hypotheses about structure-function relationships. Homology models are unreliable in predicting the conformations of insertions or deletions, i.e. portions of the sequence that don't align with the sequence of the template, as well as the details of sidechain positions. Homology models are unlikely to be useful in modeling ligand docking (drug design) unless the sequence identity with the template is >70%, and even then, less reliable than an empirical crystallographic or NMR structure.

SWISS-MODEL makes it quick and easy to submit a target sequence and get back an automatically generated homology model, provided an empirical structure with >30% sequence identity exists to use as a template. (The template will be identified automatically, and the alignment made automatically.) These automated models may be useful, but will sometimes have errors that could be avoided if manual adjustments are made to the sequence alignment by an expert. Learning to optimise your models manually would take some time.