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. Journal of Computational Chemistry (doi: 10.1002/jcc.23149).

 

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TABLE SI. Benchmark structures for protein-RNA docking (a total of 72 targets)
 Complex of bound structures Unbound structures Type Irmsd() Fnat ΔSASA

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Jmol

PDB ID

Resol.()

No. of Chains in the PDB

Protein

HETATMs

RNA

HETATMs

Protein

Resol.()

rmsd ()

HETATMs

RNA

Resol.()

rmsd ()

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.