Introduction
RNA molecules can fold into complex tertiary structures, allowing them to carry out important genetic, structural and regulatory roles inside the cell. These complex structures often contain 3-D pockets made up of several 2-D motifs that can be targeted by small molecular ligands. Indeed, many RNA structures in PDB contain bound small molecules and high-throughput experimental studies have generated large number of interacting RNA and small molecule pairs. There are considerable interests in developing small molecule therapeutics targeting viral RNAs or those involved in neurological diseases or cancer. Towards this goal, we have established a database server collecting RNA 2-D structure motifs and small molecules interactions. We further developed a computational pipeline, which takes input an RNA sequence, predicts its secondary structure, extract its 2-D motifs and searches the motif – small molecule interactions database for similar 2-D structure motifs and potential binding small molecules. We hypothesize that the query RNA putatively has similar 2-D structure motifs that will bind to similar small molecular ligands; such information will be very useful in screening for small molecule compound that potentially targets query RNA and perturbs its biological function. We demonstrated the utility of the server by querying COVID-19 virus genome sequence and finding potential matches.