The high-risk human papillomavirus oncoprotein 18 E6 (HPV18 E6) is associated with cervix cancer. This study was conducted in order to identify the transmembrane protein 87B (TMEM87B) as a novel binding protein interacting with the HPV18 E6 oncoprotein and to perform an initial bioinformatics analysis. The yeast strain AH109 was transformed with pGBKT7-HPV18 E6 and the yeast mating assay was utilized to identify the interaction between TMEM87B and HPV18 E6 in the human Hela cDNA library. TMEM87B mRNA was detected in Hela cells by using RT-PCR. The TMEM87B gene structure, genomic localization, physical and chemical characteristics, subcellular localization and functional domain were predicted, as well as the systematic evolution analysis on similar proteins among several species. In the yeast two-hybrid assay, HPV18 E6 mRNA was expressed and there was no self-activation and toxicity in the AH109 strain. The special TMEM87B mRNA expression was detected in Hela cells and the blue clones were validated by the yeast mating assay. An efficient bioinformatics analysis fundamentally identified that TMEM87B is a secretary protein, containing many phosphorylation sites and functional motifs and possibly involved in signal transduction and transcriptional control in carcinogenesis. It was indicated that the yeast two-hybrid system is efficient for screening interacting proteins. The novel gene TMEM87B may interact with HPV18 E6 and may be a potential oncogenesis target according to the bioinformatics analysis.