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