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Current work on bipartite graph-based algorithm for protein tertiary structure matching shows that the algorithm demands heavy computation and extensive processing time during graph preparation and matching. In this work, we deployed multithreading approach using OpenMP to enhance the performance of the algorithm. The experiment on dual quad core machines shows that the speedup is 4.9 on 8 threads with the minimum execution time of 121.39 seconds, before it gradually increases as more threads are added. The parallel code has successfully utilized the available multi-cores resources and it extends the capability of the algorithm to match more structures in a given time.