See the below attachment. Is that the type of study you want for your research area?

http://pubs.acs.org/doi/abs/10.1021/ci300411b

I would suggest the following articles. These are not exactly homology modelling but protein modelling in general. You might like to explore more articles from David Baker group as well.

Article Accurate design of co-assembling multi-component protein nanomaterials

Article Computational Design of Self-Assembling Protein Nanomaterial...

Article Computational Design of an Unnatural Amino Acid Dependent Me...

Hi, You can read following paper.

http://www.nature.com/nchembio/journal/v7/n11/full/nchembio.662.html

Homology modeling is a very powerful technique, when used correctly. Several "success stories" I published myself may be:

https://www.researchgate.net/publication/257750959_Analysis_of_Decapping_Scavenger_%28DcpS%29-cap_complex_using_modified_cap_analogs_reveals_molecular_determinants_for_efficient_cap_binding

https://www.researchgate.net/publication/47812191_Structural_models_of_TREK_channels_and_their_gating_mechanism

https://www.researchgate.net/publication/40107233_Structural_and_functional_characterization_of_a_novel_host_penetration-related_pectate_lyase_from_the_potato_cyst_nematode_Globodera_rostochiensis

https://www.researchgate.net/publication/7299070_In_planta_secretion_of_a_calreticulin_by_migratory_and_sedentary_stages_of_root-knot_nematode

https://www.researchgate.net/publication/40120803_Origin_distribution_and_3D-modeling_of_Gr-EXPB1_an_expansin_from_the_potato_cyst_nematode_Globodera_rostochiensis

But there are many more others.

Best regards!

Article Analysis of Decapping Scavenger (DcpS)-cap complex using mod...

Article Structural models of TREK channels and their gating mechanism

Article Structural and functional characterization of a novel, host ...

Article In Planta Secretion of a Calreticulin by Migratory and Seden...

Article Origin, distribution and 3D-modeling of Gr-EXPB1, an expansi...

kindly check the link below.. for ur question ..maybe it can answer ur ques.

AnD ALSO CHECK THE ATTACHMENT

http://pubs.acs.org/doi/abs/10.1021/jm0491804

http://www.vls3d.com/index.php/virtual-screening/comments-about-virtuel-screening?start=6

Good day Dr. Kumar,

There was a success story in the project that I am working on. Virtual screening using homology model of parasitic histone deacetylase helped to find several hits for this new target. The results of virtual screening have been recently published:

http://www.ncbi.nlm.nih.gov/pubmed/25243797

X-ray structures with hits have been also prepared and are described here:

http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003645

If you are trying to get an overview of how successful homology modeling is in general, you may have a problem with publication bias by just looking at case studies. Success is considered interesting and remarkable. Failure is less remarkable, not necessarily because it is statistically likely (this depends on how success is defined and the closeness of the templates and other factors) but because it is seen as less interesting.

To get an accurate view you need a systematic benchmark (as in the papers cited by Vijay). The article below is not quite what you asked for (structures that were modeled first then proven to be accurate by x-ray crystallography) but gives a systematic benchmark of the accuracy of  modeled structures for one specific task (docking).

https://www.researchgate.net/publication/265415512_Protein_structure_prediction_provides_comparable_performance_to_crystallographic_structures_in_docking-based_virtual_screening

Article Protein structure prediction provides comparable performance...