FP-AK-QIEA-R has been used in Benchmark Functions, Protein Folding Problem and multi-objective problems. PECO was a proposed algorithm with good performance in Protein Folding Problem. The objective of this paper is perform experiments to improve the performance of PECO using FP-AK-QIEA-R to initialize PECO. After plotting the best of ever, a meaningful change on the convergence is observed showing the modification of the convergence and after plotting the number of habitats is noticed a reduction of the number of habitats. In conclusion, adding FP-AK-QIEA-R solution improves the performance of PECO. © 2018 IEEE.