TOPSCAN is a rapid method for comparing protein structures. It is useful as a preliminary screen to give you some idea whether your protein looks like something else.
It trades coverage (and to some degree error rate) for great speed. If you want much more accurate comparisons you need to use a method which works at the detailed coordinate level such as SSAP.
How it works
TOPSCAN reduces your protein to a series of secondary structure elements (SSEs) and adds information to the SSE descriptors such as relative direction, adjacency to the previous SSE, length and length of preceeding loop. These "topology strings" are then compared against a library of topology strings built from the Protein Databank.
For details of the TOPSCAN method together with an analysis of its performance, see Martin, A. C. R. (2000) The Ups and Downs of Protein Topology; Rapid Comparison of Protein Structure , Protein Engineering, 13, 829-837.
Note! There is a typo in the paper. In Table II, the top left value (same orientation and same secondary structure) should be a 10 not a 1.
NOTE! The TOPSCAN server works at the domain level. You should only submit a single domain.