Systems and methods for storing protein structure information are provided. The system comprises a non-public database storing protein structure information, wherein the non-public database is coupled to a public database of non-proprietary protein structure information and to non-public sources of proprietary protein structure information. The non-public database may also be coupled to a database having protein structure information for substantially all the proteins of at least one organism genome. The method may comprise loading protein structure data from at least one public database and loading protein structure data from one or more proprietary sources of protein structure information. The public database may comprise the Protein Data Bank (PDB). Certain types of additional information are also advantageously loaded into the database. These may include classification data corresponding to at least one protein ontology. Mass spectroscopy data, NMR data and x-ray crystallography data may also be loaded into the database.