Arena: Rapid and accurate reconstruction of full-atomic RNA structures from coarse-grained models
Authors/Creators
- 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; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA
- 3. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
Description
Arena-main.zip contains the source code, which is also available on GitHub.
benchmarking_datasets.zip contains the datasets used for benchmarking Arena and the other RNA reconstruction programs: pdb (original files), pdb_input (original files with missing atoms added by Arena), pdb_input_C3_prime (input files with only the C3' atoms), pdb_input_glycoN (input files with only the glycosidic N1/N9 atoms), pdb_input_P (input files with only the P atoms), pdb_input_P_C1_base (input files with only the P, C1', and base atoms), pdb_input_P_ribose (input files with only the backbone atoms), NAST (files from NAST structure prediction), and SimRNA (files from SimRNA structure prediction).
fasta.zip contains the nucleotide sequences of the RNAs in the benchmarking dataset, which is a required input for Rosetta rna_thread.
lists.zip contains text files of the PDB IDs used for benchmarking.
RNA_classes.zip contains tsv files of the benchmarking dataset split by type of RNA