Described herein are methods and compositions comprising a mixture of silk polymer and hydroxyapatite. The methods described herein can be used to prepare a mixture of silk polymer and hydroxyapatite and further provide mixtures that can be molded into a desired shape. Also encompassed herein are compositions comprising a mixture of silk polymer and hydroxyapatite having a desired shape, which can further be implanted, for example, to facilitate bone healing or tooth structure or support. Such compositions can also include agents, such as therapeutic agents, or cells.