The effective combination of a bacterial Reverse Two-Hybrid System screening platform and a SICLOPPS randomised library has been previously used for the identification of cyclic peptide inhibitors of various protein-protein interactions. A more robust Reverse Two-Hybrid System was designed and constructed to utilise a fluorescent protein reporter as well as an antibiotic resistance gene and HIS3 to enable selection of an inhibitor. The functionality of the new system was tested with the HIF1[alpha]/HIF1[Beta] and p6/UEV heterodimeric interactions and the cyclic peptide inhibitors that had been previously identified for these interactions. Next, a split-intein with improved properties was used to construct a second generation SICLOPPS library, which was tested to show that it displayed more efficient splicing. The increased toxicity of the Nostoc punctiforme DnaE splitintein employed in the new library was reduced by the addition of the SsrA protein degradation tag to enable the identification of more varied cyclic peptide inhibitors in future SICLOPPS screens.