Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

Algorithm 1

Overview of the algorithm.

(1)   function find_alignments(graph)

(2)   INPUT: graph, an alignment graph between atoms from two proteins

(3)   OUTPUT: resList, a list of the largest distinct alignments found

(4)  

(5)   ResultList resList = empty_result_list()

(6)   SeedList seeds = enumerate_seeds(graph)

(7)   For each seed in seeds

(8)      VertexSet set = extend_seed(seed)

(9)      VertexSet result = empty_set()

(10)    For each vertex in set

(11)        If (is_valid(vertex))

(12)          result.add(vertex)

(13)       End If

(14)       resList.insert_if_better(result)

(15)    End For

(16) End For