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).
fasta.zip contains the nucleotide sequences of the RNAs in the benchmarking dataset, which is a required input for Rosetta rna_thread.
list is a text file of the PDB IDs in the benchmarking dataset.