Method for molecular subshape similarity matching

A database of three-dimensional molecule shapes may be effectively searched for similarity to a query molecule subshape. Triangle matching is first performed between a query subshape triangle representative of a local volume distribution within the query molecule, and a target subshape triangle representative of a local volume distribution within a target molecule of the database. Based upon overlap of the target molecule and query molecule as determined by alignment of matched subshape triangles, shape matching between the aligned query and target molecules is then performed. Comparison of a direction assigned to each vertex of the matched subshape triangles based upon a principal axis of sampled local volume, eliminates unsuitable subshape triangle pairs from consideration prior to the computationally-intensive shape matching step.