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The protein threading problem (PTP) is to determine the three-dimensional structure of a given protein sequence. Currently its serial resolutions are time-consuming and data-intensive. Nevertheless, the parallel and distributed systems offer opportunities to improve the efficiency of PTP by releasing its computational bottleneck. Therefore, a 1-level-core parallel threading algorithm is proposed and implemented in a hybrid peer-to-peer (P2P) based high performance computing (HPC) platform, P2HP-2. Through experiments and analysis, it shows that high performance can be achieved through the 1-level-core parallel algorithm in P2HP-2.