Homology modelling is the type of comparative - template based modelling. What can be the structure that homology modelling estimate - Primary, secondary, tertiary and quaternary.
This template based modelling is depend on the quality of the sequence alignment and template structure.This method of homology modelling is based on tertiary structure which is more conserved than amino acid sequences(1ry, 2nd and quaternary).
Template dependent modelling may also be dependent on the availability of resolved structure that are deposited in the protein data bank. For a quick search of homologous sequences whose structure have been resolved, you can try FUGUE (http://tardis.nibio.go.jp/fugue/prfsearch.html)
The hits that you get here may not necessarily have 100% homology with you sequence but can serve a start template. You can however also model your molecules on multiple templates using tools such as Modeller http://salilab.org/modeller/ to get a more accurate model
Besides MODELLER, I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) is a pretty good tool to produce homology models as well. It boasts having the best performance in CASP (an experiment to test the accuracy of tools), but as the other posters have mentioned the model depends highly on the template.
Phyre 2 is another for 3d structure modeling, but I don't know how to interpret the result. If anybody help I appreciate.
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