AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

RNA is considered as an attractive target for new small molecule drugs. Designing active compounds can be facilitated by computational modeling. Most of the available tools developed for these prediction purposes, such as molecular docking or scoring functions, are parametrized for protein targets. The performance of these methods, when applied to RNA-ligand systems, is insufficient. To overcome these problems, we developed AnnapuRNA, a new knowledge-based scoring function designed to evaluate RNA-ligand complex structures, generated by any computational docking method. We also evaluated three main factors that may influence the structure prediction, i.e., starting conformer of a ligand, the docking program, and the scoring function used. We applied the AnnapuRNA method for a post-hoc study of the recently published structures of the FMN riboswitch. Software is available at . Author summary Drug development is a lengthy and complicated process, which requires costly experiments on a very large number of chemical compounds. The identification of chemical molecules with desired properties can be facilitated by computational methods. Several methods were developed for computer-aided design of drugs that target protein molecules. However, recently the ribonucleic acid (RNA) emerged as an attractive target for the development of new drugs. Unfortunately, the portfolio of the computer methods that can be applied to study RNA and its interactions with small chemical molecules is very limited. This situation motivated us to develop a new computational method, with which to predict RNA-small molecule interactions. To this end, we collected the information on the statistics of interactions in experimentally determined structures of complexes formed by RNA with small molecules. We then used the statistical data to train machine learning methods aiming to distinguish between RNA-ligand interactions observed experimentally and other interactions that can be observed in theoretical analyses, but are not observed in nature. The resulting method called AnnapuRNA is superior to other similar tools and can be used to predict preferred ligands of RNA molecules and how RNA and small molecules interact with each other.