The problem of predicting sets of components of heteromeric protein complexes is a challenging problem in Systems Biology. There have been many tools proposed to predict those complexes. Among them, PPSampler, a protein complex prediction algorithm based on the Metropolis-Hastings algorithm, is reported to outperform other tools. In this work, we improve PPSampler by refining scoring functions and a proposal distribution used inside the algorithm so that predicted clusters are more accurate as well as the resulting algorithm runs faster. The new version is called PPSampler2. In computational experiments, PPSampler2 is shown to outperform other tools including PPSampler. The F-measure score of PPSampler2 is 0.67, which is at least 26% higher than those of the other tools. In addition, about 82% of the predicted clusters that are unmatched with any known complexes are statistically significant on the biological process aspect of Gene Ontology. Furthermore, the running time is reduced to twenty minutes, which is 1/24 of that of PPSampler.
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