BACKGROUND Long non-coding RNA (lncRNA) studies play an important role in the development, invasion, and metastasis of the tumor. The analysis and screening of the differential expression of lncRNAs in cancer and corresponding paracancerous tissues provides new clues for finding new cancer diagnostic indicators and improving the treatment. Predicting lncRNA-protein interactions is very important in the analysis of lncRNAs. This article proposes an Ant-Colony-Clustering-Based Bipartite Network (ACCBN) method and predicts lncRNA-protein interactions. The ACCBN method combines ant colony clustering and bipartite network inference to predict lncRNA-protein interactions. RESULTS A five-fold cross-validation method was used in the experimental test. The results show that the values of the evaluation indicators of ACCBN on the test set are significantly better after comparing the predictive ability of ACCBN with RWR, ProCF, LPIHN, and LPBNI method. CONCLUSIONS With the continuous development of biology, besides the research on the cellular process, the research on the interaction function between proteins becomes a new key topic of biology. The studies on protein-protein interactions had important implications for bioinformatics, clinical medicine, and pharmacology. However, there are many kinds of proteins, and their functions of interactions are complicated. Moreover, the experimental methods require time to be confirmed because it is difficult to estimate. Therefore, a viable solution is to predict protein-protein interactions efficiently with computers. The ACCBN method has a good effect on the prediction of protein-protein interactions in terms of sensitivity, precision, accuracy, and F1-score.