Protein-RNA docking benchmark v1.1

Reference: Pérez-Cano L, Jiménez-García B, Fernández-Recio J. A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data, Proteins. 80(7):1872-82.


The Protein-RNA benchmark v1.1 is composed of 106 cases, with 5 unbound-unbound, 4 unbound-pseudo-unbound, 62 unbound-bound, 5 unbound-model, 8 model-unbound, 19 model-bound cases and 3 model-model. The main objective of this benchmark is to foster the development of new protein-RNA docking algorithms and contribute to the better understanding and prediction of protein-RNA interactions.

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Updates and corrections

(May, 10, 2013):

  1. RNA 1M8W chain is 'c' ('c,e' before)
  2. Complex 2PY9 chains are 'a,b:e/f' ('a,b:f' before)
  3. Complex 1J2B chains are 'a,b:c/d' ('a,b:c' before)

Version 1.1 (Sep, 15, 2015):
  1. 1M8V protein sequence renumbered (thanks to Prof. Shengyou Huang)

Protein-RNA docking benchmark v1.0


Table I. Protein-RNA docking benchmark: extended set from experimental cases
Complex Protein RNA
PDBa Protein/RNA Description  Typeb PDBc RMSDd BSAe PDBc RMSDd BSAe I-RMSDf
Unbound-unbound (5 cases)      
1ASY_a,b:r/s Saccharomyces cerevisiae aspartyl-tRNA synthetase / Asp-tRNA 1 1EOV_a,b 1.4 2088 3TRA_a 5.0 2201 2.7
1DFU_p:m,n Escherichia coli ribosomal protein L25 / loop E of 5S rRNA 2 1B75_a 4.3 815 364D_b,c 3.3 841 4.7
1OB2_a:b Escherichia coli elongation factor EF-TU / Phe-tRNA 1 1EFC_a 11.2 1241 1EHZ_a 2.7 1435 10.6
1R3E_a:c,d,e Thermotoga Maritima tRNA pseudouridine synthase TruB / RNA substrate 1 1ZE1_a 5.2 1349 1EHZ_a 2.3 1537 7.2
2FMT_a:c Escherichia coli methionyl-tRNAfMet formyltransferase / formyl-methionyl-tRNAfMet 1 1FMT_a 1.2 1573 3CW5_a 2.9 1590 2.2
Unbound-pseudo-unbound (4 cases)      
1B23_p:r Thermus Aquaticus elongation factor EF-TU:GTP / E. Coli cysteinyl-tRNA 1 1TUI_a 10.0 1286 1U0B_a 6.6 1457 10.4
1MFQ_c:a Homo sapiens SRP 54kDa protein / 7S RNA of human SRP 5 1QB2_b 3.1 538 1L9A_b 5.1 539 2.5
1QTQ_a:b Escherichia coli glutaminyl-tRNA synthetase / Gln-tRNA 1 1NYL_a 1.6 2360 3KNH_y 4.6 2695 2.7
1U0B_b:a Escherichia coli cysteinyl-tRNA synthetase / Cys-tRNA 1 1LI7_a 1.0 2099 1B23_r 6.6 2302 3.6
Unbound-bound (62 cases)g      
1B7F_a:p Drosophila melanogaster sxl-lethal protein / RNA 9 3SXL_a 6.7 1348 1B7F_p 0.0 1567 6.9
1C9S_l,m,n,o,p,q,r,s,t,u,v:w Geobacillus stearothermophilus trp RNA-binding attenuation protein / ssRNA 9 1QAW_a,b,c,d,e,f,g,h,i,j,k 0.4 16466 1C9S_w 0.0 29294 0.4
1DK1_a:b Thermus thermophilus ribosomal protein S15 / 16S rRNA fragment 2 2FKX_a 2.8 1226 1DK1_b 0.0 1234 2.4
1E7K_a:c Homo sapiens spliceosomal 15.5kd protein / U4 snRNA fragment 4 2JNB_a 3.2 610 1E7K_c 0.0 659 1.8
1EC6_a:d Homo sapiens Nova-2 KH3 K-homology RNA-binding domain / RNA hairpin 8 1DTJ_a 1.6 873 1EC6_d 0.0 906 0.6
1EIY_a,b,d,e:c/f h Thermus thermophilus phenylalanyl-tRNA synthetase / Phe-tRNA 1 1JJC_a,b,d,e h 1.3 2143 1EIY_c 0.0 2272 1.8
1EKZ_a:b Drosophila melanogaster Staufen dsRBD / RNA hairpin 6 1STU_a 5.2 596 1EKZ_b 0.0 548 3.4
1F7U_a:b Saccharomyces cerevisiae arginyl-tRNA synthetase / Arg-tRNA 1 1BS2_a 3.4 2591 1F7U_b 0.0 2992 2.5
1G1X_a:d Thermus thermophilus ribosomal protein S6 / 16S rRNA fragment 2 1RIS_a 1.9 179 1G1X_d 0.0 176 2.2
1H3E_a:b Thermus thermophilus tyrosyl-tRNA synthetase / Tyr- tRNA(gua) and ATP and tyrosinol 1 1H3F_a 9.4 1223 1H3E_b 0.0 1297 0.2
1H4S_a,b:t Thermus thermophilus prolyl-tRNA synthetase / Pro-tRNA(cgg) and prolyl-adenylate analogue 1 1HC7_a,b 1.4 1123 1H4S_t 0.0 1252 0.9
1HC8_a:c Bacillus stearothermophilus ribosomal protein L11 / 23S rRNA fragment 2 1FOY_a 2.9 990 1HC8_c 0.0 984 2.5
1HVU_a,b:c Human immunodeficiency virus 1 reverse transcriptase / RNA pseudoknot 9 2VG5_a,b 5.4 621 1HVU_c 0.0 607 6.4
1JBR_b:d Aspergillus restrictus ribotoxin restrictocin / 23S rRNA sarcin-ricin domain 2 1AQZ_a 0.6 702 1JBR_d 0.0 754 0.5
1K8W_a:b Escherichia coli pseudouridine synthase TruB / T stem-loop RNA 1 1R3F_a 2.2 1407 1K8W_b 0.0 1649 1.7
1KOG_a:i Escherichia coli threonyl-tRNA synthetase / essential domain of its mRNA operator 6 1EVL_a 0.6 851 1KOG_i 0.0 862 0.5
1KQ2_a,b,h,i,k,m:r Staphylococcus aureus Hfq protein / RNA 9 1KQ1_a,b,h,i,k,m 1.4 1358 1KQ2_r 0.0 1642 1.1
1M5O_c:a,b Homo sapiens U1 small nuclear ribonucleoprotein A / RNA hairpin ribozyme and RNA substrate 3 1NU4_a 1.6 869 1M5O_a,b 0.0 950 1.8
1M8V_a,b,c,d,e,f,g:o/p/q/r/s/t/u Pyrococcus abyssii sm protein / uridine heptamer 9 1H64_a,b,c,d,e,f,g 0.6 309 1M8V_o 0.0 365 0.4
1M8W_a:c Homo sapiens pumilio-homology domain / NRE1-19 RNA 6 1M8Z_a 1.2 941 1M8W_c 0.0 1159 0.7
1MMS_a:c Thermotoga maritima ribosomal protein L11 / 23S rRNA fragment 2 2K3F_a 4.2 1200 1MMS_c 0.0 1239 3.6
1N78_a:c Thermus thermophilus glutamyl-tRNA synthetase / Glu-tRNA and glutamol-AMP 1 1J09_a 1.9 2064 1N78_c 0.0 2308 1.5
1Q2R_a:e Zymomonas mobilis catalytic tRNA guanine transglycosylase / RNA substrate 1 1R5Y_a 0.8 1232 1Q2R_e 0.0 1362 1.1
1SER_a,b:t Thermus thermophilus seryl-tRNA synthetase / Ser-tRNA 1 1SES_a,b 1.9 1095 1SER_t 0.0 1085 2.3
1T0K_a,b:c,d Escherichia coli MBP- Saccharomyces cerevisiae L30e fusion protein / pre-mRNA 6 1NMU_a,b 1.5 466 1T0K_c,d 0.0 507 3.3
1T4L_b:a Saccharomyces cerevisiae dsRBD of Rnt1p RNase III / 5' terminal RNA hairpin of snR47 precursor 4 1T4O_a 2.2 924 1T4L_a 0.0 795 1.7
1U63_a:b Methanocaldococcus jannaschii ribosomal protein L1 / mRNA fragment 2 1I2A_a 1.3 1135 1U63_b 0.0 1075 1.0
1WNE_a:b,c Foot and Mouth Disease Virus RNA-dependent RNA polymerase / template-primer RNA 6 1U09_a 0.7 1426 1WNE_b,c 0.0 1597 0.7
1WPU_a:c Bacillus subtilis Hut operon positive regulatory protein / Hut mRNA 6 1WPV_a 0.2 608 1WPU_c 0.0 700 0.2
1WSU_a:e Moorella thermoacetica C-terminal domain of elongation factor selB / SECIS RNA 6 1LVA_a 0.7 444 1WSU_e 0.0 471 0.6
1YVP_a:c,d Xenopus laevis Ro autoantigen /RNA 9 1YVR_a 1.3 1072 1YVP_c,d 0.0 1125 1.3
2AD9_a:b Homo sapiens polypyrimidine Tract Binding protein RBD1 / CUCUCU RNA 9 1SJQ_a 2.9 617 2AD9_b 0.0 760 2.3
2ADB_a:b Homo sapiens polypyrimidine Tract Binding protein RBD2 / CUCUCU RNA 9 1SJR_a 3.7 594 2ADB_b 0.0 792 2.4
2ADC_a:b/c Homo sapiens polypyrimidine Tract Binding protein RBD34 / CUCUCU RNA 9 2EVZ_a 4.2 1497 2ADC_b 0.0 1876 3.7
2ASB_a:b Mycobacterium tuberculosis NusA / BoxC stem-loop motif RNA fragment 6 1K0R_a 1.1 1076 2ASB_b 0.0 1189 0.6
2AZ0_a,b:c,d Flock House virus B2 protein / dsRNA 9 2B9Z_a,b 1.4 1090 2AZ0_c,d 0.0 1114 1.1
2AZX_a,b:c/d h Homo sapiens tryptophanyl-tRNA synthetase / Trp-tRNA 1 1R6T_a,b 1.0 1958 2AZX_c 0.0 2130 0.6
2BGG_a:p,q Archaeoglobus fulgidus piwi protein / 16nt siRNA duplex 6 1W9H_a 1.0 1008 2BGG_p,q 0.0 1179 0.9
2BH2_a:c Escherichia coli 5-methyluridine methyltransferase ruma / rRNA and s-adenosylhomocysteine 2 1UWV_a 1.4 2067 2BH2_c 0.0 2304 1.3
2BTE_a:b Thermus thermophilus leu-tRNA synthetase / Leu-tRNA and a substrate analogue 1 1H3N_a 4.1 1628 2BTE_b 0.0 1673 2.4
2BU1_a:r Bacteriophage ms2 coat protein / RNA harpin 7 2MS2_a 0.2 397 2BU1_r 0.0 445 0.1
2C0B_a,b,c,d:e/f/g/h h Escherichia coli RNase E / RNA 9 2VMK_a,b,c,d 19.3 989 2C0B_e 0.0 1034 17.9
2CZJ_a:b/d Thermus thermophilus hb8 SsrA-binding protein / tmRNA 6 1WJX_a 1.4 1799 2CZJ_b 0.0 1715 1.1
2ERR_a:b Homo sapiens RBD of Fox-1 / UGCAUGU RNA 9 2CQ3_a 3.4 840 2ERR_b 0.0 1101 0.1
2F8K_a:b SAM domain of Saccharomyces cerevisiae Vts1 / RNA ligand 9 2D3D_a 0.5 429 2F8K_b 0.0 432 0.5
2FK6_a,b:r/s h Bacillus subtilis Rnase Z / Thr-tRNA 1 1Y44_a,b 1.7 1095 2FK6_r 0.0 1162 2.1
2GIC_a,b,c,d,e,f,g,h,i,j:r,k h Vesicular stomatitis virus nucleocapsid protein / RNA 7 3PTO_a,b,c,d,e,f,g,h,i,j h 0.8 10013 2GIC_r,k 0.0 10210 0.7
2GJE_a,d:r,s Trypanosoma brucei treu927 guideRNA-binding protein / gRNA 6 2GIA_a,b 4.2 859 2GJE_r,s 0.0 836 4.2
2GJW_a,b:e,f,h Archaeoglobus fulgidus tRNA-splicing endonuclease / RNA 9 1R0V_a,b 1.6 1508 2GJW_e,f,h 0.0 1648 1.6
2HGH_a:b Xenopus laevis transcription factor IIIA zinc fingers 4-6 / 5S rRNA 55mer 2 2J7J_a 12.0 1314 2HGH_b 0.0 1201 9.0
2HW8_a:b Thermus thermophilus ribosomal protein L1 / Methanococcus vannielii mRNA fragment 6 1AD2_a 6.7 1170 2HW8_b 0.0 1207 5.7
2I91_b:e,f Xenopus laevis Ro autoantigen / misfolded pre-5S rRNA fragment 2 1YVR_a 1.2 1832 2I91_e,f 0.0 1924 1.4
2IX1_a:b Escherichia coli RNase II / RNA 10 2ID0_a 1.4 1877 2IX1_b 0.0 2106 1.0
2PY9_a,b:e/f KH1 domain of Homo sapiens poly(rC)-binding protein 2 / Homo sapiens telomeric RNA fragment 6 2JZX_a 2.5 492 2PY9_f 0.0 520 2.1
2QUX_a,b:c Pseudomonas phage pp7 coat protein / RNA harpin 7 2QUD_a,b 0.7 780 2QUX_c 0.0 900 0.3
2R7R_a:x Rotavirus RNA-dependent RNA polymerase VP1 / RNA 9 2R7Q_a 0.6 890 2R7R_x 0.0 1004 1.5
3BO2_a:b,c,d,e Homo sapiens U1 small nuclear ribonucleoprotein A / Group I intron P9 3 1NU4_a 1.7 860 3BO2_b,c,d,e 0.0 938 1.7
3BSB_b:c Homo sapiens Pumilio1 protein / CyclinB reverse RNA 6 1M8Z_a 1.8 1203 3BSB_c 0.0 1447 0.9
3BSO_a:p,t Norwalk Virus polymerase / primer-template RNA and CTP 9 1SH0_a 1.3 1513 3BSO_p,t 0.0 1670 1.5
3BSX_a:c Homo sapiens Pumilio 1 protein / Puf5 RNA 6 1M8Z_a 1.5 1205 3BSX_c 0.0 1478 0.6
3BX2_a:c Saccharomyces cerevisiae Puf4 RBD / HO endonuclease RNA 3' UTR recognition sequence 6 1M8Z_a 3.5 1100 3BX2_c 0.0 1317 1.8
3CIY_a:c,d Mus musculus Toll-like receptor 3 ectodomain / dsRNA 9 3CIG_a 1.2 1133 3CIY_c,d 0.0 1102 1.4


a PDB code of the protein-RNA complex. Protein and RNA chains are separated by colon. Alternative binding modes are separated by a slash ("/").
b Functional classification of RNA according to SCOR 1.2 database36: 1 = tRNA, 2 = rRNA, 3 = ribozyme, 4 = snRNA, 5 = SRP RNA, 6 = Genetic control elements, 7 = vRNA, 8 = SELEX RNA, 9 = synthetic RNA and 10 = other.
c PDB code of the protein or RNA subunits.
d RMSD (Å) between Cα atoms (for proteins) or phosphorous atoms (for RNA) of individual bound reference and unbound structures
e Buried Surface Area (Å2) of the unbound molecule upon complex formation (see Equation(1) in Methods)
f RMSD (Å) of interface Cα and phosphorus atoms of unbound protein and RNA structures, and the equivalent atoms in the complex.
g Unbound RNA is not available or cannot be modelled, so the bound form is used.
h The biological assembly from the PDB has been considered, therefore some of the chains in the complex have been renamed.




Table II. Protein-RNA docking benchmark: extended set from homology modeling cases
Complex Protein RNA
PDBa Protein/RNA Description  Typeb PDBc RMSDd BSAe PDBc RMSDd BSAe I-RMSDf
Unbound-model (5 cases)      
1C0A_a:b Escherichia Coli aspartyl-tRNA synthetase / Asp-tRNA 1 1EQR_a 1.6 2140 1EFW_c 2.4 2272 1.8
1EFW_a:c Thermus thermophilus aspartyl-tRNA synthetase / E. Coli Asp-tRNA 1 1L0W_a 1.3 1201 1C0A_b 1.6 1166 1.1
1J1U_a,c:b/d Methanocaldococcus jannaschii tyrosyl-tRNA synthetase / Tyr-tRNA 1 1U7D_a,b 2.4 1049 2XUY_v 2.2 1125 1.9
1J2B_a,b:c/d Pyrococcus horikoshii tRNA-Guanine Transglycosylase / lambda-form Val-tRNA 1 1IQ8_a,b 0.9 3254 2ZUF_b 10.4 3602 5.5
2DRA_a:b Archaeoglobus fulgidus CCA-adding enzyme with tRNAminiDCC and ATP 1 1R89_a 1.9 1363 1VFG_d 3.0 1613 2.1
Model-unbound (8 cases)      
1FEU_a:b,c Thermus Thermophilus ribosomal protein L25 / fragment of 5S rRNA 2 1NJP_t 4.4 789 1A4D_a,b 5.0 786 3.6
1HQ1_a:b M domain of Escherichia coli SRP Ffh protein / domain IV of 4.5S SRP RNA 5 2FFH_a 1.2 669 1CQL_a 9.5 660 4.7
1LNG_a:b Methanocaldococcus jannaschii SRP 19kDa protein / 7S.S SRP RNA 5 1KVV_a 4.1 1099 1Z43_a 2.0 1185 3.6
1OOA_a:c Mus musculus nuclear factor NF-kappa-B p105 subunit / high-affinity RNA aptamer 8 3DO7_b 6.4 951 2JWV_a 6.0 859 4.7
1RKJ_a:b N-terminal RNA-binding domains of Mesocricetus auratus nucleolin / pre-rRNA target 2 2KRR_a 10.1 1056 1QWA_a 4.9 1183 8.3
2R8S_l,h:r Mus musculus specific synthetic FAB / P4-P6 RNA ribozyme domain 3 2FJF_l,h 1.9 1181 1HR2_a 4.0 1279 2.2
2V3C_c:m Methanocaldococcus jannaschii SRP54 protein / 7S.S SRP RNA 5 3DM5_a 13.0 1371 1Z43_a 1.7 1371 12.5
2ZKO_a,b:c,d NS1 protein of human influenza virus A / dsRNA 9 2Z0A_a,b 1.0 1197 2ZI0_c,d 4.4 1182 2.6
Model-bound (19 cases)g      
1DDL_a,b,c:d Desmodium yellow mottle tymovirus coat protein / vRNA fragment 7 1AUY_a,b,c 1.1h 572 1DDL_d,e 0.0 657 0.6h
1E8O_a,b:e/c,d:e Homo sapiens SRP 9KDa and 16 Kda proteins / Alu RNA 5' domain 5 1914_a,b 1.8 519 1E8O_e 0.0 507 0.6
1FXL_a:b Homo sapiens antigen HUD RRM12 domains / fragment of the class I c-fos AU-rich element 6 3SXL_a 7.4 1139 1FXL_b 0.0 1257 7.6
1K1G_a:b Homo sapiens SF1-Bo isoform / yeast and mammalian pre-mRNA transcript intron BPS 6 2BL5_a 10.7 1142 1K1G_b 0.0 1343 11.2
1MJI_a:d/c Thermus thermophilus ribosomal protein L5 / 5S rRNA fragment 2 1IQ4_a 3.2 862 1MJI_d 0.0 828 1.1
1RLG_a:c Archaeoglobus fulgidus 50S ribosomal protein L7Ae / box C/D RNA fragment 10 1XBI_a 2.4 631 1RLG_c 0.0 625 1.6
1S03_h:a Escherichia coli ribosomal Protein S8 / spc Operon mRNA fragment 6 1SEI_a 1.6 833 1S03_a 0.0 883 1.5
2B3J_a,b:e/f Staphylococcus aureus tRNA Adenosine Deaminase / anticodon stem-loop of Arg-tRNA 1 1WWR_a,b 2.2 1011 2B3J_e 0.0 1051 2.8
2CJK_a:b Saccharomyces cerevisiae nuclear polyadenylated RBP4 / RNA 9 1L3K_a 12.8 1165 2CJK_b 0.0 1450 13.1
2CSX_a:c Aquifex aeolicus methionyl-tRNA synthetase / Met-tRNA 1 2D5B_a 2.2 1023 2CSX_c 0.0 1093 2.1
2D6F_a,b,c,d:e/f Methanothermobacter thermautotrophicus Glutamyl-tRNA amidotransferase/Glu-tRNA 1 1ZQ1_a,b,c,d 2.9 616 2D6F_e 0.0 602 3.7
2DB3_a:e Drosophila melanogaster DEAD-box protein Vasa / ssRNA 9 2I4I_a 15.8 492 2DB3_e 0.0 678 16.5
2DER_b:d Escherichia coli tRNA-specific 2-thiouridylase mnmA / Glu-tRNA 1 2HMA_a 2.8 1125 2DER_d 0.0 1281 3.3
2DLC_a,b:y/z i Saccharomyces cerevisiae tyrosyl-tRNA synthetase / Tyr-tRNA 1 1N3L_a,b i 6.1 999 2DLC_y 0.0 1052 4.4
2FY1_a:b Homo sapiens RNA-binding motif protein Y / S1A stem-loop RNA 8 1X5S_a 5.5 1072 2FY1_b 0.0 1117 3.1
2I82_a:e Escherichia coli pseudouridine synthase / anticodon stem loop of Phe-tRNA 1 1XPI_a 4.9 1476 2I82_e 0.0 1666 5.4
2IPY_a:c Oryctolagus cuniculus Iron-responsive element-binding protein 1 / ferritin IRE-RNA 6 2B3Y_a 11.8 1331 2IPY_c 0.0 1411 8.4
2JPP_a,b:c/d Pseudomonas fluorescens RsmE / Shine-Dalgarno sequence of hcnA mRNA 6 1Y00_a,b 4.9 970 2JPP_c 0.0 1039 4.2
2NUG_a:c,d,e,f RNase III from Aquifex aeolicus / dsRNA 9 1O0W_a 14.2 1479 2NUG_c,d,e,f 0.0 1473 12.0
Model-model(3 cases)      
1QF6_a:b Escherichia coli threonyl-trna synthetase complexed with its cognate tRNA 1 1NYQ_a 4.1 2231 3FOZ_c 3.9 2269 3.2
1VFG_a:c Aquifex aeolicus tRNA nucleotidyltransferase / primer tRNA and an incoming ATP analog 1 3H38_a 4.0 422 1EIY_c 3.1 397 4.7
2DU3_a,b,c,d:e,f i Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase / Cys-tRNA and O-phosphoserine 1 2DU7_a,b,c,d 4.5 631 2ZZN_d 3.1 709 3.7

a PDB code of the protein-RNA complex. Protein and RNA chains are separated by colon. Alternative binding modes are separated by a slash ("/").
b Functional classification of RNA according to SCOR 1.2 database (36): 1 = tRNA, 2 = rRNA, 3 = ribozyme, 4 = snRNA, 5 = SRP RNA, 6 = Genetic control elements, 7 = vRNA, 8 = SELEX RNA, 9 = synthetic RNA and 10 = other.
c PDB code of the protein or RNA subunits. Cases in which the protein or RNA has been modelled, the PDB of the template is shown. In italics are shown cases with pseudo-unbound templates, i.e. bound to a different protein or RNA molecule (see main text).
d RMSD (Å) between Cα atoms (for proteins) or phosphorous atoms (for RNA) of individual bound reference and unbound structures
e Buried Surface Area (Å2) of the unbound molecule upon complex formation (see Equation(1) in Methods)
f RMSD (Å) of interface Cα and phosphorus atoms of unbound protein and RNA structures, and the equivalent atoms in the complex.
g Unbound RNA is not available or cannot be modelled, so the bound form is used.
h The 24 Nt residues have not been considered for the RMSD calculation as they are swapped between target and template structures and give high RMSDs that do not reflect the true overall quality.
i The biological assembly from the PDB has been considered, therefore some of the chains in the complex have been renamed.