%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Models analyzed in Das, Karanicolas, Baker 
"Atomic accuracy in predicting and designing
noncanonical RNA structure" [Table 1 and Fig. 1].
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


This directory contains:


1. A legend, "RNA_descriptions.txt", also copy/pasted below that describes the correspondence of the motif name to its PDB source and a more complete description used in Table 1.

2. Experimental structures for 32 RNA motifs, e.g.: 

  chunk002_1q9a_RNA.pdb

3. A log file obtained from clustering the 500 best scoring decoys from FARFAR denvo runs, e.g.:

  cat_chunk002_1q9a_5kcycles_decoys_nonativefrags.out.cluster_rms.out






chunk001_uucg 1F7Y UUCG tetraloop 
chunk002_1csl 1CSL Rev response element high affinity site
chunk002_1lnt 1LNT Signal recognition particle Domain IV
chunk003_1q9a 1Q9A GAGA tetraloop from sarcin/ricin loop 
chunk001_157d 157D G-A base pair
chunk001_1kd5 1KD5 Helix with A/C base pairs
chunk001_255d 255D Helix with U/C base pairs
chunk001_359d 359D Pre-catalytic conformation, hammerhead ribozyme
chunk001_1kh6 1KH6 Four-way junction, HCV IRES
chunk006_1jj3 1JJ2 Kink-turn motif
chunk002_2oeu 2OEU Tertiary interaction, hammerhead ribozyme
chunk003_2eew 2EEW L2/L3 tertiary interaction, purine riboswitch
chunk003_2gis 2GIS Kink-turn motif from SAM-I riboswitch
chunk003_2r8s 2R8S J4/5 from P4-P6 domain, Tetrahymena ribozyme
chunk005_2eew 2EEW Three-way junction, purine riboswitch
chunk004_2oiu 2OIU Stem C internal loop, L1 ligase
chunk001_lopE 354D Loop E motif, 5S RNA
chunk002_1d4r 1D4R Fragment with G/G and G/A pairs, SRP helix VI
chunk002_1q9a 1Q9A Bulged G motif, sarcin/ricin loop 
chunk099_2r8s 2R8S Tetraloop/receptor, P4-P6 domain, Tetr. ribozyme
chunk001_1d4r 1D4R Fragment with A/C pairs, SRP helix VI
chunk001_1u9s 1U9S Loop 8, A-type Ribonuclease P
chunk001_283d 283D Curved helix with G/A and A/A base pairs
chunk099_1mhk 1MHK Hook-turn motif
chunk003_1xjr 1XJR Pentaloop from conserved region of SARS genome
chunk003_2oeu 2OEU Active site, hammerhead ribozyme
chunk003_2gdi 2GDI L3, thiamine pyrophosphate riboswitch
chunk003_2qwy 2QWY P1/L3, SAM-II riboswitch
chunk004_2r8s 2R8S J5/5a hinge, P4-P6 domain, Tetr. ribozyme
chunk005_2qbz 2QBZ J4a/4b region, metal-sensing riboswitch
chunk013_2oiu 2OIU Tetraloop/helix interaction, L1 ligase crystal
chunk099_3b31 3B31 Pseudoknot, domain III, CPV IRES
