RLDOCK: A New Method for Predicting RNA-Ligand Interactions.

ABSTRACT: The ability to accurately predict the binding site, binding pose, and binding affinity for ligand-RNA binding is important for RNA-targeted drug design. Here, we describe a new computational method, RLDOCK, for predicting the binding site and binding pose for ligand-RNA binding. By developing an energy-based scoring function, we sample exhaustively all of the possible binding sites with flexible ligand conformations for a ligand-RNA pair based on the geometric and energetic scores. The model distinguishes from other approaches in three notable features. First, the model enables exhaustive scanning of all of the possible binding sites, including multiple alternative or coexisting binding sites, for a given ligand-RNA pair. Second, the model is based on a new energy-based scoring function de

SUBMITTER: Sun LZ 

PROVIDER: S-EPMC7882445 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature