Figure 1

Flowchart of CPSARST. CPSARST uses a 'double filter-and-refine' strategy combining a fast screening and an accurate refinement step, each having two different rounds. In the screening stage, the three-dimensional structure of the query protein is transformed into a one-dimensional structural string by a RST algorithm [40]. This query string is subjected to two rounds of database searches. In round 1, it is searched against a pre-transformed structural string database by a heuristic method. In round 2, it is duplicated prior to the database search. Results of the two rounds are filtered; hits with meaningfully improved similarity scores are considered as CP candidates (colored red). In the refinement stage, candidates are analyzed by an accurate structural alignment algorithm, FAST [63], with and without CP manipulation, to determine their reliabilities and to retrieve permutation sites more precisely. After filtering out improbable cases, final answers with detailed information are output. The example used in this figure is a real case with simplified hit lists.