<abstract> <p>Ribonucleic acid (RNA) structure alignment is an important problem in computational biology to identify structural similarity of RNAs. Obtaining an efficient method for this problem is challenging due to the high computational time for the optimal solution and the low accuracy of a heuristic solution. In this paper, an efficient algorithm is proposed based on a mathematical model called longest arc-preserving common subsequence. The proposed algorithm uses a heuristic technique and high-performance computing to optimize the solution of RNA structure alignment, both in terms of the running time and the accuracy of the output. Extensive experimental studies on a multicore system are conducted to show the effectiveness of the proposed algorithm on two types of data. The first is simulated data that consists of 450 comparisons of RNA structures, while the second is real biological data that consists of 357 comparisons of RNA structures. The results show that the proposed algorithm outperforms the best-known heuristic algorithm in terms of execution time, with a percentage improvement of 71% and increasing the length of the output, i.e., accuracy, by approximately 45% in all studied cases. Finally, future approaches are discussed.</p> </abstract>