title: Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.
abstract: RNA molecules play integral roles in gene regulation, and understanding their structures gives us important insights into their biological functions. Despite recent developments in template-based and parameterized energy functions, the structure of RNA--in particular the nonhelical regions--is still difficult to predict. Knowledge-based potentials have proven efficient in protein structure prediction. In this work, we describe two differentiable knowledge-based potentials derived from a curated data set of RNA structures, with all-atom or coarse-grained representation, respectively. We focus on one aspect of the prediction problem: the identification of native-like RNA conformations from a set of near-native models. Using a variety of near-native RNA models generated from three independent methods, we show that our potential is able to distinguish the native structure and identify native-like conformations, even at the coarse-grained level. The all-atom version of our knowledge-based potential performs better and appears to be more effective at discriminating near-native RNA conformations than one of the most highly regarded parameterized potential. The fully differentiable form of our potentials will additionally likely be useful for structure refinement and/or molecular dynamics simulations.
authors.affiliation: INRIA AMIB Bioinformatique, Laboratoire d'Informatique (LIX), Ecole Polytechnique, 91128 Palaiseau, France. julie.bernauer@inria.fr
authors.forename: Julie
authors.initials: J
authors.lastname: Bernauer
authors.forename: Xuhui
authors.initials: X
authors.lastname: Huang
authors.forename: Adelene Y L
authors.initials: AY
authors.lastname: Sim
authors.forename: Michael
authors.initials: M
authors.lastname: Levitt
mesh_terms: D018360:Crystallography, X-Ray; D051188:Knowledge Bases; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA