Predicting RNA-small molecule binding sites by 3D structure

The prediction of RNA-small molecule binding sites is crucial for the discovery of effective drugs. Various computational methods have been developed to address this challenge, using information about the structure and sequence of RNA. In this study, we introduce CplxCavity, a combination of a new algorithm and a machine learning model specifically designed to predict RNA-small molecule binding sites. CplxCavity leverages the 3D structure of RNA or RNA complexes to identify surface cavities that have the potential to bind with small molecules. Our results demonstrate that CplxCavity outperforms existing methods by accurately identifying binding sites for small molecules on RNA or RNA complexes. The introduction of CplxCavity represents a significant advancement in computational tools for studying RNA-ligand interactions, and offers promising prospects for accelerating drug discovery and the development of therapies targeting RNA.