Arena: Rapid and Accurate Reconstruction of Full Atomic RNA Structures From Coarse-grained Models
Affiliation:
1. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA;2. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA;3. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA;4. Department of Chemistry, Yale University, New Haven, CT 06511, USA;5. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
Abstract:
RNA tertiary structures from experiments or computational predictions often contain missing atoms, which prevent analyses requiring full atomic structures. Current programs for RNA reconstruction can be slow, inaccurate, and/or require specific atoms to be present in the input. We present Arena (Atomic Reconstruction of RNA), which reconstructs a full atomic RNA structure from residues that can have as few as one atom. Arena first fills in missing atoms and then iteratively refines their placement to reduce nonideal geometries. We benchmarked Arena on a dataset of 361 RNA structures, where Arena achieves high accuracy and speed compared to other structure reconstruction programs. For example, Arena was used to reconstruct full atomic structures from a single phosphorus atom per nucleotide to, on average, within 3.63 Å RMSD of the experimental structure, while virtually removing all clashes and running in <3 s, which is 353× and 46× faster than state-of-the-art programs PDBFixer and C2A, respectively. The Arena source code is available at https://github.com/pylelab/Arena and the webserver at https://zhanggroup.org/Arena/.
