RNA molecules have highly versatile structures that can fold into myriad conformations, providing many potential pockets for binding small molecules. The increasing number of available RNA structures, in complex with proteins, small ligands and in free form, enables the design of new therapeutically useful RNA-binding ligands. Here we studied RNA ligand complexes from 10 RNA groups extracted fr...

Structure based drug discovery on GPCRs harness atomic detail X-ray binding pockets and large libraries of potential drug lead candidates in virtual screening (VS) to identify novel lead candidates. Relatively small conformational differences between such binding pockets can be critical to the success of VS. Retrospective VS on GPCR/ligand co-crystal structures revealed stark differences in the...

In this work, we propose a network-based approach to cluster the protein pockets into similar groups in a database level. A pocket similarity network is constructed to describe structural similarity relationships among the pockets from the systematic perspective, which possesses the community structures and can can be utilized to develop a direct method to cluster the pockets by partitioning th...