A similarity search method includes generating a feature database which stores data pertaining to a candidate molecule, as executed by a processor of a computer, the database including a hash table having entries which are generated based on, a set of descriptors generated from conformations of fragment graphs of the candidate molecule, the fragment graphs including plural fragment nodes connected by rotatable bond edges, a specific conformation of the fragment node including a fragment of the candidate molecule, and two neighboring fragments connected by a rotatable bond at a specific dihedral angle including a fragment pair, and a context-adapted descriptor-to-key mapping which maps the set of descriptors to a set of feature keys including indices that label grid cells in discriminant space.