RNA-RNA Docking Benchmark 1.0

@ Huang Lab

Click here to download the zipped benchmark package

Reference: Yan Y, Huang SY. RRDB: A comprehensive and nonredundant benchmark for RNA-RNA docking and scoring. Bioinformatics. 2017, doi: 10.1093/bioinformatics/btx615. [PDF]

Table S1:  The benchmark dataset for RNA-RNA docking (123 cases)
Target RNA 1 RNA2 Interface
PDB_Chain(s)a Descriptionb Chain(s) Name Strand type Length rmsd (Å)c HETATMs Chain(s) Name Strand type Length rmsd (Å)c HETATMs Typed rmsd (Å)c ΔSA (Å2)e
Easy (47 cases)                              
  1BJ2_A:B RNA loop-loop complex 2BJ2_A RNA (synthetic) double 21 1.191   1BJ2_B RNA (synthetic) double 19 0.000 U/B 0.673 992
  1KD5_A:B r(GGUCACAGCCC)2 metal free form 1KD3_A RNA (synthetic) single 11 0.365   1KD4_A RNA (synthetic) single 11 2.062 U/U 1.481 1106
  1KIS_A:B TAR-TAR "kissing" hairpin complex 2RN1_A RNA (synthetic) double 16 2.431   1KIS_B RNA (synthetic) double 16 0.000 U/B 1.488 856
  1KOC_A:B RNA aptamer 1KOD_A RNA (synthetic) single 11 0.850   1KOC_B RNA (synthetic) double 14 0.000 U/B 0.564 1351
  1MIS_A:B anti-parallel RNA duplex with tandem G:A mismatches 2XXA_F 4.5s RNA  single 8 1.172   2O81_A RNA (synthetic) single 8 1.609 U/U 1.408 784
  1NTA_A:B Streptomycin RNA-aptamer 1NTB_A RNA (synthetic) single 22 0.530   1NTA_B RNA (synthetic) single 18 0.000 U/B 0.393 2222
  1RRR_A:B RNA duplex containing a purine-rich strand 404D_A RNA (synthetic) single 10 1.370   1DRR_B RNA (synthetic) single 10 1.196 U/U 1.286 920
  1T0E_A:C 2-aminopurine labelled bacterial decoding site RNA 1T0E_A RNA (synthetic) single 18 0.000   1T0D_B RNA (synthetic) single 17 1.325 B/U 0.909 1723
  1X9K_AB:CD An all-RNA Hairpin Ribozyme with mutation U39C 1X9K_AB RNA (synthetic) double 26 0.000   2OUE_CD Loop B ribozyme strand  double 36 0.588 B/U 0.435 1558
  1Y0Q_A:B an active group I ribozyme-product complex 1Y0Q_A Group I ribozyme  double 229 0.000   2Z75_B glmS ribozyme RNA  single 4 0.299 B/U 0.098 926
  1YLS_A:B selenium-modified Diels-Alder ribozyme 1YKV_A Diels-Alder ribozyme  single 11 0.428 CSL,UMS 1YKQ_B Diels-Alder ribozyme  double 38 0.843 UMS,CSL U/U 0.735 1188
  259D_A:B the RNA duplex [r(CCCCGGGG)]2 1G2J_A RNA (synthetic) single 8 1.389   1RXA_A RNA (synthetic) single 8 0.610 U/U 1.072 871
  2D17_A:B stem-bulge-stem region of the HIV-1 dimerization initiation site 2D1A_A RNA  single 16 1.141   2D1B_A RNA  single 14 0.753 U/U 0.979 1450
  2GCS_A:B the Thermoanaerobacter tengcongensis glmS ribozyme 2Z75_A glmS ribozyme substrate RNA  single 21 0.197 2AD 2Z74_B glmS ribozyme RNA  double 123 0.424 A23 U/U 0.447 3078
  2MXK_A:B 19-nt duplex 2MXK_A RNA (synthetic) single 9 0.000   2MXL_A RNA (39-mer)  single 10 1.908 B/U 1.384 990
  2OUE_AB:CD a junctionless all-RNA hairpin ribozyme 1X9C_AB RNA (synthetic) double 25 0.313 A2M 2P7E_CD Ribozyme strand II  double 36 0.292 U/U 0.230 1445
  2P7E_ABP:CD Vanadate at the Active Site of a Small Ribozyme 2P7D_ABP 5' substrate strand, pentameric fragment  double 26 0.246 S9L,AVC 2OUE_CD Loop B ribozyme strand  double 36 0.292 U/U 0.210 1615
  2Q1O_A:B the RNA Dodecamer CGC-NF2-AAUUGGCG 2G92_A RNA (synthetic) single 12 0.819 NF2 2Q1O_A RNA (synthetic) single 12 0.290 NF2 U/B 0.614 1228
  2QUW_A:B Hammerhead Ribozyme G12A mutant after cleavage 2QUS_A Hammerhead ribozyme  single 12 0.268 CCC,GTP 2QUW_B Hammerhead ribozyme, cleaved fragment  double 57 0.000 U/B 0.138 1671
  2R20_A:B the RNA brominated tridecamer r(GCGUU-5BUGAAACGC) 2R1S_A RNA (synthetic) single 13 0.084 5BU 2R22_A RNA (synthetic) single 13 0.787 5BU U/U 0.560 1261
  2RN1_A:B the kissing complex formed by the apical loop of the HIV TAR RNA and an RNA aptamer 1KIS_A RNA (synthetic) double 16 2.431   2RN1_B RNA (synthetic) double 16 0.000 U/B 1.476 987
  2V6W_A:B tRNASer acceptor stem 1M5O_B RNA hairpin ribozyme  single 7 0.571   4YCP_B tRNATrp  single 7 1.001 U/U 0.815 666
  2V7R_A:B a human tRNAGly microhelix 5MMI_A 23S ribosomal RNA  single 7 1.480   4NHA_B RNA (synthetic) single 7 0.957 U/U 1.246 710
  2VUQ_A:B a human tRNAGly acceptor stem microhelix 2VUQ_A RNA (synthetic) single 7 0.000   5DM6_X 23S ribosomal RNA  single 7 2.008 B/U 1.420 697
  2XSL_A:B a Thermus thermophilus tRNAGly acceptor stem microhelix 5AOX_C ALU jo consensus RNA  single 7 1.902   3DIL_A RNA (174-mer)  single 7 0.568 U/U 1.403 719
  2YIE_X:Z a F. nucleatum FMN riboswitch 3F2Q_X FMN riboswitch  double 54 0.872 GTP 5KX9_Y FMN Riboswitch  double 57 0.784 GTP U/U 0.842 5382
  357D_BC:A fragment I from E. coli 5S rRNA 357D_BC RNA (synthetic) double 50 0.000   5GAE_B 5S rRNA  single 11 1.681 SSU B/U 1.073 1147
  3B5S_AB:C Hinged Hairpin Ribozyme 3CR1_AB RNA (synthetic) double 43 0.433 S9L,A2M 2OUE_D Loop B S-turn strand  single 19 0.251 N6G U/U 0.309 2602
  3CGP_A:B a pseudouridine-containing yeast spliceosomal U2 snRNA-intron branch site duplex 3CGS_A RNA (synthetic) single 12 0.898 PSU 3CGQ_B RNA (synthetic) single 13 0.215 U/U 0.641 1105
  3FS0_A:B Class II ligase ribozyme product-template duplex 3PDR_A M-box Riboswitch RNA  single 10 1.093   3FS0_B RNA (synthetic) single 11 0.000 U/B 0.733 1113
  3G78_A:Z group II intron 4E8Q_A Group IIC intron  double 389 0.823   3G78_Z Ligated EXON product  single 9 0.000 U/B 0.644 1100
  3IGI_A:B the Oceanobacillus Iheyensis Group II Intron 4E8Q_A Group IIC intron  double 389 0.817   3IGI_B RNA (synthetic) single 9 0.000 U/B 0.594 1084
* 3JQ4_A:B the complex of the large ribosomal subunit 1NKW_0 23S ribosomal RNA  double 2765 1.242   5DM6_Y 5S ribosomal RNA  double 118 0.916 U/U 1.133 1708
  3SKI_A:B the 2'- Deoxyguanosine riboswitch 3SLQ_A RNA (68-mer)  double 68 0.860 CCC,GTP 3SKZ_A RNA (68-mer)  double 68 0.861 CCC U/U 0.391 787
  3ZP8_A:B high-resolution full-length hammerhead ribozyme 3ZD5_A hammerhead ribozyme, enzyme strand  double 43 0.315 GDP 2OEU_B RNA (synthetic) single 20 0.326 OMC U/U 0.319 2542
  434D_A:B  tRNA(Ala) acceptor stem   3VJR_B tRNA CCA-acceptor  single 7 1.081   4UYK_R SRP RNA  single 7 0.742 U/U 0.927 697
  4E59_A:B GCCGCCGC duplex 4KNQ_B RNA (synthetic) single 8 1.281   3ADD_C selenocysteine tRNA  single 8 0.445 U/U 0.959 580
  4FAW_A:B Oceanobacillus iheyensis group II intron 4FAQ_A Group IIC intron  double 390 0.880   2Z75_B glmS ribozyme RNA  single 5 1.645 U/U 0.698 791
  4MCF_C:D the Gas5 GRE Mimic 4MCE_A Gas5 GREM Fwd  single 9 0.322   4MCF_B Gas5 GREM Rev  single 11 0.067 U/B 0.226 929
  4TS0_X:Y the Spinach RNA aptamer 4TS2_X Spinach aptamer RNA, bimolecular construct  double 44 0.595 CCC 4TS0_Y Spinach RNA aptamer, bimolecular construct  double 46 0.000 U/B 0.416 4581
  4U3L_A:B octameric RNA duplex 4U78_A RNA (synthetic) single 8 0.228   4U47_A RNA (synthetic) single 8 0.851 U/U 0.623 929
  5DQK_A:B the hammerhead ribozyme cleavage reaction-WT ribozyme 5DI4_A RNA (48-mer)  double 48 0.474   5DH6_B RNA (synthetic) single 20 0.244 U/U 0.408 1893
  5EW4_A:B C9ORF72 Antisense CCCCGG repeat RNA 5EW7_A RNA (synthetic) single 20 0.204   5EW4_B RNA (synthetic) single 21 0.000 U/B 0.142 1751
* 5FJ1_B:C the standard kink turn HmKt-7 4BW0_A HMKT-7  double 24 1.302   5FJ1_A hmkt-7  double 24 0.262 U/B 0.528 762
  5HNJ_A:B the 5-Formylcytosine in RNA Duplex 5JAJ_X RNA (synthetic) single 8 0.988 RSQ 5JB2_X RNA (synthetic) single 8 1.043 RSQ U/U 1.016 750
  5J02_A:B the Oceanobacillus iheyensis group II intron 4FAQ_A Group IIC intron  double 414 2.563   5J02_B 5' EXON ANALOG RNA (synthetic) single 7 0.000 6F7 U/B 0.906 1218
  5L00_A:B Self-complimentary RNA 15mer 5KRG_A RNA (synthetic) single 15 0.224 LCC,LCG 5V0H_A RNA (synthetic) single 15 0.773 LCC,LCG U/U 0.569 1394
Medium (38 cases)                              
  1A3M_A:B the a site of 16s rRNA 1BYJ_A RNA (16S RNA)  single 14 1.024   1FYO_A fragment of 18S ribosomal RNA  single 13 3.758 U/U 2.710 1407
  1C4L_A:B an RNA duplex including a C-U base-pair 4LCK_C T-box riboswitch stem I  single 9 3.771   1C4L_B RNA (synthetic) single 9 0.000 U/B 2.666 877
  1ELH_A:B helix I from the 5s RNA of Escherichia Coli 5GAE_B 5S rRNA  single 12 1.577   5GAD_B 5S rRNA  single 13 3.634 U/U 2.880 1180
  1FUF_A:B a 14bp RNA oligonucleotide containing double UU bulges 1IK5_A RNA (synthetic) single 14 0.219 CBR 433D_A RNA (synthetic) single 14 3.995 CBR U/U 2.829 1821
  1LMV_A:B the unmodified U2 snRNA-intron branch site helix from S. cerevisiae 1LPW_A RNA (synthetic) single 9 0.969   3JB9_Q RNA (synthetic) single 10 3.115 U/U 2.307 869
  1NUJ_A:B the leadzyme structure 1LDZ_A lead-dependent ribozyme  single 13 3.861   429D_B RNA (synthetic) single 11 0.185 U/U 2.792 1036
  1QC0_A:B a 19 base pair copy control related RNA duplex 4WFL_A RNA  single 9 2.728   1QC0_B RNA (synthetic) single 10 0.000 U/B 1.878 917
  1SAQ_A:B the RNA octamer GIC(GA)GCC 1U6B_B 197-mer RNA single 8 1.750   1WZ2_C tRNA  single 8 2.204 U/U 1.990 933
  1XV0_A:B RNA internal loop with three consecutive sheared GA pairs 3PDR_A M-box Riboswitch RNA  single 10 3.061   2VQE_A 16s rRNA  single 10 2.244 P5P U/U 2.662 1303
  1ZEV_A:B a Pathogenic RNA: CUG Repeats 5MWI_A RNA G(CUG)8C duplex  single 18 2.117   4JNX_B RNA (synthetic) single 18 2.374 U/U 2.249 1795
  1ZX7_A:B decoding-site RNA  2A04_A RNA (synthetic) single 15 2.294   1ZZ5_B RNA (synthetic) single 14 1.933 U/U 2.127 1408
  2ADT_A:B a 30 kDa GAAA tetraloop-receptor complex. 2I7E_A 43-mer RNA double 43 0.978   2I7Z_A 43-mer RNA double 43 2.226 U/U 1.518 1486
  2IRN_A:B (rGCUGAGGCU)2 and (rGCGGAUGCU)2 5MMI_W 4.5S ribosomal RNA  single 9 2.198   5H1S_C Spinach chloroplast 4.5S rRNA  single 9 2.214 U/U 2.206 1038
  2K3Z_A:B adenosine bulged RNA duplex with C:G-A triple 2K3Z_A RNA (synthetic) single 9 0.000   1VQ8_0 23S ribosomal RNA  single 8 2.815 B/U 1.931 828
  2K41_A:B uridine bulged RNA duplex 5MMI_A 23S ribosomal RNA  single 9 2.496   1VQ8_0 23S ribosomal RNA  single 8 2.597 U/U 2.544 849
  2K65_A:B the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma) 2PXV_B 4.5 s RNA  single 7 0.859   3TUP_T Thermus thermophilus tRNAPhe  single 7 2.791 U/U 2.065 679
  2M1O_A:B ID3 stem 2AHT_A 27-mer RNA single 7 3.973   3WBM_X RNA (25-mer)  single 7 0.896 U/U 2.880 696
  2M23_A:B the d3'-hairpin of the group II intron Sc.ai5gamma 2M1V_A RNA (29-mer)  double 29 2.612   3TUP_T Thermus thermophilus tRNAPhe  single 7 3.735 U/U 2.960 906
  2O83_A:B Tandem GA RNA Pairs 4Y1M_A E. coli yybP-ykoY riboswitch  single 9 3.593  IC, IG 2O83_A RNA (synthetic) single 9 0.133  IC, IG U/B 2.543 905
  2OOM_A:B a kissing complex formed between the TAR RNA element of HIV-1 and a LNA/RNA aptamer 2JLT_B TAR RNA double 16 2.376   2PN9_B RNA 16-mer with locked residues 9-10  double 16 2.385 LCA,10C U/U 1.828 861
  2W89_A:B the E.coli tRNAArg aminoacyl stem issoacceptor RR-1660 4LVW_A THF riboswitch  single 7 1.975   1D6K_B 5S rRNA E-loop (5SE)  single 7 1.503 U/U 1.755 714
  354D_A:B loop E FROM E. coli 5S rRNA 1DFU_N 5s rRNA  single 12 0.322   1A51_A 5s rRNA loop d/loop e  single 12 2.256 G46 U/U 1.611 1447
  3B58_BC:A Junctioned Hairpin Ribozyme 3B91_BC 29-mer Loop A and Loop B Ribozyme strand  double 49 0.984 S9L 4WFA_X 23S rRNA  single 13 2.938 U/U 1.809 2070
  3GLP_A:B r(GCUGCUGC)2 5EMF_A RNA (synthetic) single 8 1.709   5MWI_A RNA G(CUG)8C duplex  single 8 1.763 U/U 1.736 777
  3NJ7_A:B r(GGCAGCAGCC)2 3NJ6_A RNA (synthetic) single 10 0.884   2XXA_F 4.5S RNA  single 10 2.322 U/U 1.757 999
  3P22_A:B the ENE in complex with A9 RNA 3P22_A Core ENE hairpin from KSHV PAN RNA  double 40 0.000 GTP 4OQ8_B RNA (synthetic) single 9 5.540 B/U 2.489 1856
  3P4C_A:B modified 2'Fluoro RNA octamer f/rA2U2-R32 4NGD_B RNA (synthetic) single 8 2.445 CFZ,AF2,UFT 4NGC_B RNA (synthetic) single 8 1.502 CFZ,AF2,UFT U/U 2.029 674
  3R1E_A:B GC(8BrG)GCGGC duplex 4KTG_B RNA (synthetic) single 8 1.119 GRB 2ZUE_B tRNA-Arg  single 8 1.896 GRB U/U 1.557 802
  3TD0_A:B the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site 3TD1_A RNA (synthetic) single 21 2.004 5BU 4P3S_B RNA (synthetic) single 23 2.497 5BU U/U 2.270 2066
  439D_A:B an RNA duplex with an unusual G.C pair 5DDP_A RNA (61-mer)  single 8 2.599   4XWF_A PFL RNA  single 8 0.610 U/U 1.887 901
  472D_A:B an octamer RNA with tandem gg/uu mispairs 2PXF_B 4.5 s RNA  single 8 2.363   472D_B RNA (synthetic) single 8 0.000 U/B 1.671 776
* 4E8K_A:B Oceanobacillus iheyensis group II intron 4E8Q_A Group IIC intron  double 388 0.944   5GAD_A 23S rRNA  single 7 4.499 U/U 1.822 1037
  4MSR_A:B RNA 10mer duplex with six 2'-5'-linkages 4MS9_A Native RNA duplex 10mer  single 10 1.610   5TDJ_A RNA (synthetic) single 10 1.557 U/U 1.584 1136
  4PCO_A:B double-stranded RNA with four terminal GU wobble base pairs 2PXB_B 4.5 s RNA  single 10 2.144   2PXU_B 4.5 s RNA  single 10 2.436 U/U 2.295 1001
  4RKV_A:B UGGGGU quadruplexes 1J8G_A RNA (synthetic) single 6 0.213   3RG5_A tRNA(Sec)  single 6 2.417 U/U 1.537 651
  4RNE_AB:CD UGGGGU quadruplexes 1RAU_AB RNA (synthetic) double 12 2.959   4RNE_AB RNA (synthetic) double 12 0.150 U/B 2.095 968
* 5FJ0_A:B the standard kink turn HmKt-7 4CS1_A RNA (synthetic) single 19 2.056   4C40_A RNA (synthetic) single 19 2.134 U/U 2.096 2682
* 5G4T_A:B a quasi-cyclic six k-turn duplex RNA species 5FJ4_D HMKT-7  single 11 0.706   1FKA_A 16S ribosomal RNA  single 8 2.651   U/U 1.844 1326
Difficult (38 cases)                              
  1AJL_A:B five-nucleotide bulge loop from tetrahymena thermophila group i intron 2R8S_R p4-p6 RNA ribozyme domain  single 12 8.164   5MMI_A 23S ribosomal RNA  single 7 3.541 U/U 6.753 942
  1D4R_A:B fragment of human srp RNA helix 6 1JID_B helix 6 of human SRP RNA  single 29 25.116 GDP,A23 1L9A_B signal recognition particle RNA S domain  single 29 25.852 GDP U/U 25.480 2690
  1DQH_A:B helix II of the X. laevis somatic 5s rRNA with a cytosine bulge 1DQF_A RNA (synthetic) single 9 0.555   4WC2_B RNA 75-mer  single 10 7.641 U/U 5.556 908
  1JZV_A:B a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA 2Z75_B glmS ribozyme RNA  single 8 5.624 5BU 1JZV_B RNA (synthetic) single 9 0.000 5IC U/B 3.858 831
  1LNT_A:B the Highly Conserved RNA Internal Loop of SRP 28SP_A conserved motif in SRP RNA  single 12 1.568 CBV 1GAX_C tRNA(val)  single 12 4.724 CBV U/U 3.457 1407
  1N53_A:B B. subtilis T box antiterminator RNA 1N53_A RNA (synthetic) single 16 0.000   3BNT_A A site of human mitochondrial ribosome  single 9 6.822 B/U 4.093 1283
  1NYI_A:B Crosslinked Hammerhead Ribozyme Initial State 3D0M_X RNA (synthetic) single 16 11.650   1Q29_B Ribozyme  double 24 0.924 U/U 7.911 2031
  1QCU_A:B an 18 base pair copy control related RNA duplex 3PU1_R RNA (45-mer)  single 11 6.849   3PU0_R RNA (45-mer)  single 11 7.102 U/U 6.976 1102
  1SDR_A:B an RNA dodecamer 1SDR_A RNA (synthetic) single 12 0.000   3IEV_D RNA (synthetic) single 12 6.107 B/U 4.224 1169
  1TUT_A:B J4/5 Loop from the Candida albicans and Candida dubliniensis Group I Introns 5MMI_A 23S ribosomal RNA  single 11 5.795   1TUT_B RNA (synthetic) single 11 0.000 U/B 4.098 1236
  280D_A:B an RNA dodecamer 1RNG_A RNA (synthetic) single 12 10.511   280D_A RNA (synthetic) single 12 0.614 U/B 7.445 1222
  2D1A_A:B the HIV-1 dimerization initiation site in the extended-duplex dimer 2D1B_A RNA  double 39 29.878   2D1A_A RNA  single 39 2.909 U/B 21.227 3667
  2DD2_A:B  a RNA duplex with  A6/A15/A16 stack 1U6B_B 197-mer RNA single 10 6.249   2VQE_A 16s rRNA  single 10 2.170 P5P U/U 4.678 1260
  2FQN_A:B the Homo sapiens cytoplasmic ribosomal decoding A site 4K31_B RNA (synthetic) single 22 3.421   4K32_A RNA (synthetic) single 21 2.574 U/U 3.037 2040
  2G91_A:B the an RNA nonamer r(GGUGCGC)d(BrC)r(C) 3W3S_B selenocysteine tRNA  single 9 5.458 CBR 2G91_A RNA (synthetic) single 8 1.281 CBR U/B 4.068 829
  2JXS_A:B RNA duplex containing single adenosine bulge 1GAX_C tRNA(val)  single 11 5.461   5IT9_i Cricket paralysis virus IRES RNA  single 10 1.858 U/U 4.155 1015
  2K7E_A:B the human tRNALys3 bound to the HIV genome Loop I 2K7E_A RNA (synthetic) single 12 0.000   1FEQ_A RNA (synthetic) single 12 6.941 PSU,SUR B/U 4.908 1094
  2KXZ_A:B RNA Internal Loops with Tandem AG Pairs: 5'AAGU/3'UGAA 2LX1_A RNA (synthetic) single 11 5.481   2KXZ_A RNA (synthetic) single 11 0.622 U/B 3.901 1096
  2L1F_A:B a conserved retroviral RNA packaging element 1S9S_A MLV Psi encapsidation site  double 65 14.165   1U6P_B 101-mer RNA double 66 14.785 U/U 17.776 2358
  2P89_A:B the 3' pseudouridyation pocket of U65 snoRNA 2EUY_A U65 box H/ACA snoRNA  double 34 7.430   2P89_B 28S rRNA  single 14 0.000 U/B 5.283 1786
  2PCW_A:B an rRNA Substrate Bound to the Pseudouridylation Pocket of a Box H/ACA snoRNA 2PCV_A U65 Box H/ACA snoRNA  double 35 11.536   5AN9_N 26S ribosomal RNA  single 14 7.438 U/U 8.542 1452
* 2XEB_A:B the protein-unbound spliceosomal u4 snRNA 5' stem loop 2OZB_C RNA comprising the 5' Stem-Loop RNA of U4snRNA  single 19 6.973   2XEB_B RNA (synthetic) single 14 0.000 U/B 5.230 1728
  364D_AC:B fragment I from E. coli 5s rRNA 364D_AC RNA (synthetic) double 42 0.000 1SC 5GAE_B 5S rRNA  single 19 4.309 B/U 3.047 2222
  397D_A:B the HIV-1 trans-activation response region RNA stem 1LVJ_A HIV-1 Trans Activating Region RNA  single 15 4.909   1AJU_A TAR RNA  single 12 1.994 U/U 3.479 1207
  3B31_A:B domain III of the Cricket Paralysis Virus IRES RNA 3MJA_B Domain 3 of the cricket paralysis virus intergenic region IRES RNA  double 29 1.587   5IT9_i Cricket paralysis virus IRES RNA  single 14 10.411 U/U 4.223 997
  3C3Z_A:B HIV-1 subtype F DIS extended duplex RNA 1ZCI_A RNA (synthetic) single 23 18.220 UMS 3C7R_A HIV-1 subtype F genomic RNA  single 23 1.013 UMS U/U 12.903 2542
  3CGR_A:B the pseudouridylated U2 snRNA and intron branch site consensus sequences 1VQ8_0 23S ribosomal RNA  single 12 4.410 PSU 3CGR_B RNA (synthetic) single 13 0.000 U/B 3.055 1133
  3FTM_A:B Class II ligase ribozyme product-template duplex 5DM6_X 23S ribosomal RNA  single 11 6.730   3FTM_B RNA (synthetic) single 12 0.000 U/B 4.654 1231
  3GVN_A:B an E.coli tRNASer acceptor stem microhelix 1SDS_D box H/ACA sRNA  single 7 4.953   3GVN_B RNA (synthetic) single 7 0.000 U/B 3.503 715
  3P59_A:B an RNA Nanosquare 2PN4_A RNA (synthetic) single 15 1.631 5BU 2ZUE_B tRNA-Arg  single 10 9.113 U/U 6.013 817
  3TZR_A:B a Riboswitch-like RNA-ligand complex 5A2Q_3 hcv ires  single 20 7.403   3TZR_B RNA (synthetic) single 16 0.000 U/B 5.518 1853
  422D_A:B the dodecamer r(GAUCACUUCGGU)  3JB9_N U6 snRNA  single 12 9.850   1HLX_A RNA (synthetic) single 12 7.395 U/U 8.552 739
  4JRD_A:B the parallel double-stranded helix of poly(A) RNA 3PTX_R RNA (45-mer)  single 11 5.978   4PLX_A Core ENE hairpin and A-rich tract from MALAT1  single 11 3.864 U/U 5.033 1897
  4MCE_A:B the Gas5 GRE Mimic 1VQ8_0 23S ribosomal RNA  single 10 1.012   5G2X_A group ii intron  single 10 6.456 U/U 4.621 981
  4P97_A:B ligand-responsive RNA switches 5CNR_A RNA (synthetic) single 16 1.180   3DW5_A Sarcin/Ricin Domain from E. Coli 23 S rRNA  single 11 9.889 U/U 6.494 1237
  4R0D_A:B a eukaryotic group II intron lariat 4R0D_A group iib intron lariat  double 617 0.000   5GAE_A 23S rRNA  single 14 12.893 B/U 5.685 2309
  5CNR_A:B self-assembling RNA nano triangles 4P97_A RNA (synthetic) single 16 1.180   3S8U_A Ecoli 23 S rRNA Sarcin Ricin loop  single 11 5.852 U/U 3.628 1024
  5D8T_A:B RNA octamer containing (S)-5' methyl, 2'-F U. 2VPL_B fragment of mRNA for l1-operon single 8 5.296 CBV,U5M 1U63_B 49 nt fragment of mRNA for l1  single 8 5.567 CBV,U5M U/U 5.433 800
a. The chain IDs of interacting RNAs following the PDB code is separated by ^":". The ^* ̄ before a PDB ID indicated the presense of a kink-turn for the target.
b. The description for the RNA complexes or structures.
c. The rmsd was calculated based on C4¨ atoms after optimal superimposition of bound and unbound structures.
d. The symbol ^U/U stands for the unbound/unbound cases, and ^U/B or ^B/U ̄ for the unbound/bound or bound/unbound cases.
e. ΔSA stands for the change of solvent access surface areas of RNAs upon complex formation, in which SA is calculated by the program FreeSASA. 



huanglab@hust.edu.cn, Lab of Biophysics and Molecular Modeling