You can check these related questions, some interesting resources have been posted there:

https://www.researchgate.net/post/Suggest_protein_structure_prediction_tools

https://www.researchgate.net/post/How_to_predict_the_3D_structure_of_a_protein_without_having_a_crystal13

Also, you can check this review. Maybe some of the tools reported there can be useful:

http://www.spandidos-publications.com/ijmm/28/3/295

Hi,

please try the Phyre2 software. Its rather self-explaining:

http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

Dear,

you may go for COFACTOR>

It first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein–ligand binding interactions, Enzyme Commission number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. it is best best for protein–ligand binding site predictions.

http://zhanglab.ccmb.med.umich.edu/COFACTOR.