Described herein are systems and methods that efficiently search for documents related to chemical structures of interest to a user. In certain embodiments, text data and chemical structure data provided in a user query are simultaneously searched with a text-based search method to efficiently produce search results. Subsequent structure-based searching on the results of the text-based search produces precise results for a particular user query. This approach increases the speed of the structure-based search by reducing the amount of data the structure-based search searches over. Additionally described herein are systems and methods for indexing document data in order to facilitate this efficient searching.