Protein-RNA Docking Benchmark

Download the benchmark version 1.0 (a gzipped tar ball file)

Download the following table in Excel format

Reference:

1. Sheng-You Huang, Xiaoqin Zou, A non-redundant structure dataset for benchmarking protein-RNA computational docking. J Comput Chem. 2013;34:311-318.)
TABLE SI. Benchmark structures for protein-RNA docking (a total of 72 targets)
　Complex of bound structures Unbound structures Type Irmsd(Å) Fnat ΔSASA
PDB ID Resol.(Å) No. of Chains in the PDB Protein HETATMs RNA HETATMs Protein Resol.(Å) rmsd (Å) HETATMs RNA Resol.(Å) rmsd (Å) HETATMs
　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
Easy (49): 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
1C0A_A:B  2.40 2 Aspartyl tRNA synthetase 　 Aspartyl tRNA 　 1IL2_A  2.60 0.945 　 1EFW_C  3.00 1.770 　 PBU/RBU 0.972 0.861 4175
1DFU_P:MN  1.80 3 Ribosomal protein l25 　 5S rRNA fragment 　 3OFQ_V  3.10 0.784 　 1FEU_CB  2.30 4.548 　 PBU/RBU 1.001 0.696 1688
1E8O_CD:E  3.20 5 Signal recognition particle protein 　 7SL RNA 　 1E8O_AB  3.20 0.930 　 1RY1_E  N/A 0.001 　 PBU/RB 0.654 0.900 1434
1F7Y_A:B  2.80 2 30S ribosomal protein S15 　 16S ribosomal RNA fragment 　 2VQE_O  2.50 0.803 　 1DK1_B  2.80 0.275 　 PBU/RBU 0.589 0.963 2427
1FFY_A:T  2.20 2 Isoleucyl-tRNA synthetase 　 Isoleucyl-tRNA 　 1QU3_A  2.90 1.367 　 1QU2_T  2.20 0.000 　 PBU/RB 0.840 0.879 4971
1G1X_FH:IJ  2.60 10 30S ribosomal protein S6, S18 　 16S ribosomal RNA fragment PSU, 5MU 2VQE_FR  2.50 0.557 　 1G1X_DE  2.60 1.678 PSU, 5MU PBU/RBU 1.059 0.879 2282
1GAX_B:D  2.90 4 Valyl-tRNA synthetase 　 tRNA(Val) 　 1GAX_A  2.90 0.411 　 1IVS_C  2.90 0.547 　 PBU/RBU 0.426 0.904 5193
1H4S_AB:T  2.85 3 Prolyl-tRNA synthetase 　 tRNApro(cgg) 　 1HC7_AB  2.43 1.385 　 1H4Q_T  3.00 0.188 　 PBU/RBU 0.840 0.773 2481
1HQ1_A:B  1.52 2 signal recognition particle protein 　 4.5S RNA domain IV 　 3LQX_A  1.93 0.470 　 1DUL_B  1.80 0.127 　 PBU/RBU 0.371 0.957 1364
1J1U_A:B  1.95 2 Tyrosyl-tRNA synthetase 　 tRNA(Tyr) 　 1U7D_A  2.65 1.272 　 　 　 PBU/RB 1.014 0.833 1113
1JBS_A:C  1.97 4 Restrictocin 　 Sarcin/Ricin domain RNA analog OMC, A2M, OMG, OMU 1JBR_A  2.15 0.628 　 1JBT_C  2.70 0.520 　 PBU/RBU 0.637 0.844 1267
1JID_A:B  1.80 2 Signal recognition particle protein 　 Helix 6 of human srp RNA 5BU, A23 3KTV_B  3.80 0.637 　 1L1W_A NMR 1.967 　 PBU/RBU 1.062 0.907 1362
1K8W_A:B  1.85 2 tRNA Pseudouridine Synthase B 　 T Stem-Loop RNA FHU 1R3F_A  1.85 1.924 　 1ZL3_B  2.80 0.229 UD5 PBU/RBU 1.398 0.800 2607
1KOG_CD:K  3.50 16 Threonyl-tRNA synthetase 　 Threonyl-tRNA synthetase mRNA 　 1EVL_AB  1.55 0.658 　 1KOG_I  3.50 0.958 　 PBU/RBU 0.775 0.827 2709
1LNG_A:B  2.30 2 Signal recognition particle protein 　 7S.S srp RNA 　 3NDB_A  3.00 0.624 　 2V3C_M  2.50 2.005 　 PBU/RBU 0.952 0.868 2367
1MMS_A:C  2.57 4 Ribosomal protein L11 　 23S ribosomal RNA fragment PSU, 5MU 2JQ7_A  NMR 1.798 　 1OLN_C  NMR 0.000 PSU, 5MU PBU/RB 1.254 0.791 2455
1N78_B:D  2.10 4 Glutamyl-tRNA synthetase 　 tRNA(Glu) 　 1J09_A  1.80 2.126 　 2DXI_C  2.20 0.905 PQ1 PBU/RBU 1.883 0.824 4570
1Q2R_C:F  2.90 6 Queuine tRNA-ribosyltransferase MSE a stem-loop RNA substrate 　 1R5Y_A  1.20 0.731 　 1Q2S_E  3.20 0.487 　 PBU/RBU 1.051 0.770 2677
1QTQ_A:B  2.25 2 Glutaminyl-tRNA synthetase 　 tRNA Gln II FHU 1GTR_A  2.50 0.403 　 1QRS_B  2.60 0.600 FHU PBU/RBU 0.381 0.937 5183
1R3E_A:CDE  2.10 4 tRNA pseudouridine synthase B 　 a stem-loop RNA 　 1ZE2_A  3.00 0.925 　 　 　 PBU/RB 0.618 0.942 3276
1S03_H:A  2.70 4 30S ribosomal protein S8 　 spc Operon mRNA 　 3OFO_H  3.10 1.165 　 1S03_B  2.70 1.631 　 PBU/RBU 0.988 0.830 1743
1SJ3_P:R  2.20 2 Small nuclear ribonucleoprotein A 　 Precursor form of the Hepatitis Delta virus ribozyme 　 1M5O_C  2.20 0.385 　 1VC7_B  2.45 0.366 　 PBU/RBU 0.383 0.898 1867
1T0K_B:CD  3.24 4 60S ribosomal protein L30 　 mRNA 　 3O58_Z  4.00 1.389 　 　 PBU/RB 0.901 0.758 1008
1YVP_B:EF  2.20 8 60-kDa SS-A/Ro ribonucleoprotein 　 Y RNA sequence, first strand, second strand IU 1YVR_A  1.95 1.437 　 1YVP_CD  2.20 0.311 IU PBU/RBU 1.514 0.875 1538
2AKE_A:B  3.10 2 Tryptophanyl-tRNA synthetase 　 transfer RNA-Trp H2U, G7M, PSU, QUO, 5MU, 4SU 2DR2_A  3.00 0.273 　 2AZX_C  2.80 3.304 H2U, 2MA, G7M, PSU, QUO, 5MU, 4SU PBU/RBU 0.692 0.976 1122
2ANR_A:B  1.94 2 Neuro-oncological ventral antigen 1 　 RNA aptamer hairpins 　 　 　 2ANN_B  2.30 0.549 　 PB/RBU 0.252 0.921 1219
2AZ0_AB:CD  2.60 4 B2 protein MSE double-stranded RNA (dsRNA) 5BU 2B9Z_AB  NMR 1.391 MSE 2AZ2_CD  2.60 0.466 　 PBU/RBU 1.122 0.721 1969
2BH2_A:C  2.15 4 23S rRNA (uracil-5-)-methyltransferase RumA 　 23S ribosomal RNA fragment 5BU 1UWV_A  1.95 1.413 　 2BH2_D  2.15 1.047 5BU PBU/RBU 1.359 0.738 4043
2CSX_B:D  2.70 4 Methionyl-tRNA synthetase 　 tRNA(Met) FMU 2CSX_A  2.70 0.335 MSE 2CT8_C  2.70 1.026 FMU PBU/RBU 0.477 0.855 2249
2CZJ_E:F  3.01 8 SsrA-binding protein 　 tmRNA 　 1WJX_A  1.70 1.488 　 2CZJ_B  3.01 0.566 　 PBU/RBU 1.145 0.821 2424
2DU3_A:D  2.60 3 O-phosphoseryl-tRNA synthetase 　 tRNA 　 2DU5_A  3.20 0.390 　 2DU4_C  2.80 0.625 　 PBU/RBU 0.423 0.875 1405
2FK6_A:R  2.90 2 Ribonuclease Z 　 tRNA(Thr) 　 1Y44_A  2.10 0.730 MSE 　 　 PBU/RB 0.939 0.950 1531
2GJW_AB:EFH  2.85 10 tRNA-splicing endonuclease 　 a bulge-helix-bulge RNA 　 1R0V_AB  2.00 1.646 　 　 　 PBU/RB 1.547 0.804 2889
2QUX_DE:F  2.44 18 Coat protein 　 a viral RNA A23 2QUD_AB  1.60 0.751 　 2QUX_C  2.44 0.483 A23 PBU/RBU 0.615 0.840 1673
2RFK_A:DE  2.87 6 Probable tRNA pseudouridine synthase B 　 Guide RNA 1, Guide RNA 2 　 3LWR_A  2.20 0.972 　 3HJY_CD  3.65 2.580 　 PBU/RBU 1.092 0.813 3068
2XDB_A:G  2.55 2 a protein toxin (ToxN) 　 a specific RNA antitoxin (ToxI) 　 2XD0_A  3.00 0.404 　 　 　 PBU/RB 0.319 0.947 1883
2ZM5_A:C  2.55 4 tRNA delta(2)-isopentenylpyrophosphate transferase 　 tRNA(Phe) A23 3FOZ_A  2.50 0.546 　 2ZXU_C  2.75 0.185 A23 PBU/RBU 0.335 0.971 3935
2ZNI_AB:C  3.10 4 Pyrrolysyl-tRNA synthetase 　 Bacterial tRNA 　 2ZNJ_AB  2.50 1.458 　 2ZNI_D  3.10 1.066 　 PBU/RBU 1.219 0.798 3887
2ZUE_A:B  2.00 2 Arginyl-tRNA synthetase 　 tRNA-Arg 　 　 2ZUF_B  2.30 0.270 　 PB/RBU 0.127 0.992 4592
3CIY_A:CD  3.41 4 Toll-like receptor 3 MSE double-stranded RNA 　 3CIG_A  2.66 1.196 　 　 　 PBU/RB 1.367 0.833 2184
3DD2_H:B  1.90 3 Thrombin heavy chain 　 an RNA aptamer 　 1GJ5_H  1.73 0.394 　 　 　 PBU/RB 0.275 0.854 1508
3EPH_A:E  2.95 4 tRNA isopentenyltransferase 　 tRNA CFL, UFT 3EPK_A  3.20 0.248 　 3EPJ_E  3.10 0.409 CFL, UFT PBU/RBU 0.229 0.967 4815
3FOZ_A:C  2.50 4 tRNA delta(2)-isopentenylpyrophosphate transferase 　 tRNA(Phe) 　 2ZXU_A  2.75 0.530 　 2ZM5_C  2.55 0.711 　 PBU/RBU 0.351 0.928 4053
3HHZ_O:R  3.50 11 Nucleocapsid protein 　 viral genomic RNA (vRNA) 　 3PTX_A  3.00 1.568 　 2GIC_R  2.92 0.971 　 PBU/RBU 0.867 0.763 2164
3LRR_A:CD  2.15 4 Probable ATP-dependent RNA helicase DDX58 　 double-stranded RNA CCC 3LRN_A  2.60 0.401 MSE 　 　 PBU/RB 0.348 1.000 664
3LWR_ABC:DE  2.20 5 Pseudouridine synthase Cbf5, Ribosome biogenesis protein Nop10, 50S ribosomal protein L7Ae 　 H/ACA RNA ATP 3LWP_ABC  2.50 0.259 　 3HJW_DE  2.35 0.794 ATP PBU/RBU 0.394 0.917 5190
3MOJ_B:A  2.90 2 ATP-dependent RNA helicase dbpA 　 23S ribosomal RNA fragment 　 2G0C_A  1.70 1.029 　 　 　 PBU/RB 0.916 0.774 1758
3OL9_M:NO  2.25 16 Polymerase 　 Positive-strand RNA 　 3OL6_A  2.50 0.561 　 3OLB_BC  2.41 0.390 　 PBU/RBU 0.376 0.965 3665
3OVB_A:C  1.95 4 CCA-Adding Enzyme 　 tRNA GDP 3OV7_A  3.00 0.328 　 3OUY_C  2.69 0.472 　 PBU/RBU 0.352 0.924 2754
　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
Medium (16): 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
1F7U_A:B  2.20 2 Arginyl-tRNA synthetase 　 tRNA(Arg) H2U, 1MG, 5MC, 2MG, PSU, 1MA, 5MU, M2G 1BS2_A  2.75 3.393 　 1F7V_B  2.90 0.876 H2U, 1MG, 5MC, 2MG, PSU, 1MA, 5MU, M2G PBU/RBU 2.573 0.800 5139
1IL2_A:C  2.60 4 Aspartyl-tRNA synthetase 　 Aspartyl transfer RNA H2U, 1MG, 5MC, PSU, 5MU 1EQR_A  2.70 1.813 　 1ASY_R  2.90 1.545 H2U, 1MG, 5MC, PSU, 5MU PBU/RBU 1.696 0.671 4086
1R9F_A:BC  1.85 3 Core protein P19 MSE small interfering RNA 　 　 　 3CZ3_EF  3.23 4.464 　 PB/RBU 2.096 0.711 1723
1RC7_A:BCDE  2.15 5 Ribonuclease III 　 double-stranded RNA (dsRNA) H2U, PSU, 5MU 1YYO_A  2.90 3.397 　 1DI2_CDEF  1.90 1.079 H2U, PSU, 5MU PBU/RBU 3.781 0.462 1866
1SER_AB:T  2.90 3 Seryl-tRNA synthetase 　 tRNAser 　 1SES_AB  2.50 1.936 　 　 　 PBU/RB 2.411 0.419 2259
1UN6_C:E  3.10 5 Transcription factor IIIA 　 5S ribosomal RNA fragment 　 2HGH_A  NMR 2.337 MSE 1UN6_F  3.10 2.571 　 PBU/RBU 2.181 0.659 1750
2BTE_D:E  2.90 4 Aminoacyl-tRNA synthetase MLZ tRNA(Leu) transcript with anticodon cag 　 1H3N_A  2.00 3.900 　 2BYT_B  3.30 1.854 　 PBU/RBU 2.758 0.679 3575
2FMT_A:C  2.80 4 Methionyl-tRNA fMet formyltransferase 　 Formyl-methionyl-tRNAfMet2 　 1FMT_A  2.00 1.168 　 3CW5_A  3.10 3.358 　 PBU/RBU 2.462 0.418 2941
2NUG_AB:CDEF  1.70 6 Ribonuclease III 　 double-stranded RNA 　 2NUF_AB  2.50 3.512 　 　 　 PBU/RB 3.047 0.608 5932
2UWM_A:C  2.31 4 Selenocysteine-specific elongation factor 　 SECIS mRNA 　 1LVA_A  2.12 7.787 　 1WSU_E  2.30 0.617 　 PBU/RBU 3.190 0.654 932
2VPL_A:B  2.30 4 50S ribosomal protein L1 　 Fragment of mRNA for L1-operon containing regulator L1-binding site H2U, OMC, PSU, 5MU, 4SU 2OV7_A  2.30 1.249 　 1U63_B  3.40 3.678 H2U, OMC, PSU, 5MU, 4SU PBU/RBU 1.703 0.506 2341
2ZKO_AB:CD  1.70 4 Non-structural protein 1 　 double-stranded RNA (dsRNA) 　 2Z0A_AB  1.85 2.728 　 2ZI0_CD  2.82 4.294 　 PBU/RBU 3.874 0.522 2466
2ZZM_A:B  2.65 2 Uncharacterized protein MJ0883 　 tRNA(Leu) 　 2ZZN_A  2.95 1.857 　 　 PBU/RB 1.581 0.733 4491
3ADD_A:C  2.40 4 L-seryl-tRNA(Sec) kinase MSE Selenocysteine tRNA 　 3ADC_A  2.90 2.625 MSE 3ADB_C  2.80 0.781 　 PBU/RBU 2.327 0.500 2942
3FTF_A:CD  2.80 3 Dimethyladenosine transferase 　 16S rRNA fragment 　 3FTD_A  1.44 2.410 　 3FTE_CD  3.00 2.327 　 PBU/RBU 2.460 0.783 1693
3HL2_C:E  2.81 5 O-phosphoseryl-tRNA(Sec) selenium transferase 　 tRNASec 　 3HL2_A  2.81 0.214 　 3A3A_A  3.10 4.008 　 PBU/RBU 2.598 0.421 975
　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
Difficult (7): 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
1H3E_A:B  2.90 2 tyrosyl-tRNA synthetase 　 Wild-type tRNAtyr(Gua) PSU, MAD, 5MU 1H3F_A  2.00 9.444 　 　 　 PBU/RB 11.454 0.143 2224
1OOA_B:D  2.45 4 Nuclear factor NF-kappa-B p105 subunit MSE RNA aptamer 　 1NFK_A  2.30 6.193 　 2JWV_A  NMR 5.444 　 PBU/RBU 5.564 0.354 1742
1U0B_B:A  2.30 2 Cysteinyl-tRNA synthetase 　 Cysteinyl tRNA 　 1LI5_A  2.30 1.001 　 1B23_R  2.60 7.303 　 PBU/RBU 4.257 0.347 4558
2HW8_A:B  2.10 2 50S ribosomal protein L1 　 mRNA 　 1AD2_A  1.90 6.727 　 1ZHO_B  2.60 1.518 H2U, MIA, PSU, 5MU, 4SU PBU/RBU 5.305 0.595 2334
2IPY_A:C  2.80 4 Iron-responsive element-binding protein 1 　 Ferritin IRE RNA 　 2B3Y_A  1.85 11.737 　 2IPY_D  2.80 0.606 　 PBU/RBU 8.601 0.317 2857
2R8S_HL:R  1.95 3 Fab heavy chain, Fab light chain 　 p4-p6 RNA ribozyme domain 　 3IVK_AB  3.10 5.609 　 1HR2_A  2.25 4.345 　 PBU/RBU 3.585 0.393 2510
2V3C_C:M  2.50 6 Signal recognition 54 kDa protein 　 7S.S SRP RNA 　 3NDB_B  3.00 13.863 　 1LNG_B  2.30 2.005 　 PBU/RBU 13.256 0.165 2876
a The chain IDs of the interacting protein and RNA in a complex is separated by ``:'', in which the former chain stands for the protein and the later chain is for the RNA.

b The column is left blank when there is no unbound structure. In this case, the bound structure is used for unbound docking in the benchmark dataset.

c ``PBU/RBU'' stands for the subset of targets in which both the protein (P) and the RNA (R) are represented in the dataset in bound and unbound conformations, and ``PB/RBU'' for the subset in which  the protein is only found in bound conformation, and the RNA is present in bound and unbound conformations. Similarly with ``PBU/RB''.

d ∆SASA stands for the change of solvent access surface areas (SASA) of the protein and the RNA upon complex formation, in which SASA is calculated by the program NACCESS.

e The structure of 1RY1 is reported to be constructed by molecular modeling based on the structure solved to 12 Å by cryo-electron microscopy.

f The "rmsd" for unbound protein/RNA structures stands for the global root mean square deviation (RMSD) between the unbound structure and its  corresponding bound structure after optimal superimpositon.

g The "Irmsd" for the unbound complex is the binding inerface RMSD between the unbound and bound complexes after optimal superimpositon with the interface atoms.