Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction

RNAs are fundamental in living cells and perform critical functions determined by their tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem. We present a novel method, DRfold, to predict RNA tertiary structures by simultaneous learning of local frame rotations and geometric restraints from experimentally solved RNA structures, where the learned knowledge is converted into a hybrid energy potential to guide RNA structure assembly. The method significantly outperforms previous approaches by >73.3% in TM-score on a sequence-nonredundant dataset containing recently released structures. Detailed analyses showed that the major contribution to the improvements arise from the deep end-to-end learning supervised with the atom coordinates and the composite energy function integrating complementary information from geometry restraints and end-to-end learning models. The open-source DRfold program with fast training protocol allows large-scale application of high-resolution RNA structure modeling and can be further improved with future expansion of RNA structure databases. Here the authors developed an open-source program (DRfold) for RNA tertiary structure prediction from sequence. Through a unique combination of end-to-end learning and geometry restraint guided simulations, the method demonstrates advantage over peer methods.