NMR Analysis of RNA Bulged Structures: Tabu Search Application in NOE Signal Assignment

Assigning NMR spectra of irregular RNAs by heuristic algorithms

“…According to the author's knowledge, they were primarily dedicated to regular cases and only one of them [22] has been tested on the structures containing bulges. The latter approach, based upon tabu search, has been used in this work.…”

“…Several heuristic approaches have been proposed to solve the assignment problem for NMR spectra of protein and RNA structures [6][7][8][9][10][11][12][17][18][19][20][21][22][23]. According to the author's knowledge, they were primarily dedicated to regular cases and only one of them [22] has been tested on the structures containing bulges.…”

“…For the considered implementation, its length has been experimentally determined and set to N/2 + 18, where N is the number of NOESY graph vertices. Further details concerning the algorithm can be found in [21,22].…”

“…Thus, a few methods have been developed especially for RNA assignment. They take advantage of exhaustive search [18,19], evolutionary algorithm [2,20], tabu [21,22] and beam search [23] strategies, and they have been applied to process the spectra recorded for regular duplex structures and small bulged duplexes. This paper is focused on the problem of resonance assignment considered for structures of irregular regions, generally understood as loops -the most common motifs occurring in RNA.…”