Supplementary Information for
Vreven, T, Moal, IH, Vangone, A, Pierce, BG, Kastritis, PL, Torchala, M, Chaleil, R, Jimenez-Garcia, B, Bates, PA, Fernandez-Recio, J, Bonvin, AMJJ and Weng, Z.,
Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2. (Journal of Molecular Biology, 2015, vol. 427, p. 3031-41)
Guest, JD, Vreven, T, Zhou, J, Moal, I, Jeliazkovd, JR, Gray, JJ, Weng, Z and Pierce, BG
An Expanded Benchmark for Antibody-Antigen Docking and Affinity Prediction Reveals Insights into Antibody Recognition Determinants (submitted)
This work is licensed under a Creative Commons Attribution 4.0 International License
Also see the GitHub repository of the Pierce lab
Download cleaned-up PDB files for the benchmark in a gzipped archive Download Table in excel file
Follow the "info" link in the leftmost column to view bound/unbound chain BLAST alignments and
potentially useful comments about individual benchmark cases
Table: Protein-Protein Docking Benchmark 5.5          
+Info Complex Cat.a PDBid 1 Protein 1 HETATMs PDBid 2 Protein 2 HETATMs RMSDb(Å) DASAc(Å2) Multimer
               
  Rigid-body (162)                  
info 1AHW_AB:C AA 1FGN_LH Fab 5g9   1TFH_A Tissue factor   0.69 1899
info 1DQJ_AB:C AA 1DQQ_CD Fab Hyhel63   3LZT_ HEW lysozyme   0.75 1765
info 1E6J_HL:P AA 1E6O_HL Fab   1A43_ HIV-1 capsid protein p24   1.05 1245
info 1JPS_HL:T AA 1JPT_HL Fab D3H44   1TFH_B Tissue factor   0.51 1852
info 1MLC_AB:E AA 1MLB_AB Fab44.1   3LZT_ HEW lysozyme   0.6 1392
info 1S78_DC:A AA 1L7I_HL pertuzumab (Perjeta)   2A91_A ErbB2   1.13 2175
info 1VFB_AB:C AA 1VFA_AB Fv D1.3   8LYZ_ HEW lysozyme   1.02 1383
info 1WEJ_HL:F AA 1QBL_HL Fab E8   1HRC_ Cytochrome C HEM,ACE 0.31 1177
info 2FD6_HL:U AA 2FAT_HL Plasminogen receptor antibody   1YWH_A Plasminogen activator receptor   1.07 1139
info 2I25_N:L AS 2I24_N Shark single domain antigen receptor   3LZT Lysozyme   1.21 1425
info 2VIS_AB:C AA 1GIG_LH Fab   2VIU_ACE Flu virus hemagglutinin   0.8 1296 Ligand Trimer Created
info 2VXT_HL:I AA 2VXU_HL Murine reference antibody 125-2H FAB   1J0S_A(6) Interleukin-18   1.33 2163
info 2W9E_HL:A AA 2W9D_HL ICSM 18 FAB fragment   1QM1_A Prion protein fragment   1.13 1677
info 3EOA_LH:I AA 3EO9_LH Efalizumab FAB fragment   3F74_A Integrin alpha-L I domain   0.39 1272
info 3HMX_LH:AB AA 3HMW_LH Ustekinumab FAB   1F45_AB Interleukin-12   0.73 1841
info 3MJ9_HL:A AA 3MJ8_HL HL4E10   3MJ6_A JAML   1.48 2457
info 3MXW_LH:A AA 3MXV_LH Anti-Shh 5E1 chimera FAB fragment   3M1N_A Sonic Hedgehog N-terminal domain   0.48 1696
info 3RVW_CD:A AA 3RVT_CD 4C1 FAB   3F5V_A DER P 1 allergen   0.5 1383
info 3SE8_HL:G AA 5JXA_HL VRC03   3TGT_A HIV 93TH057 gp120   1.22 2690
info 3U7Y_HL:G AA 3U7W_HL NIH45-46   3TGT_A HIV 93TH057 gp120   0.84 2544
info 3WD5_HL:ABC AA 4NYL_HL adalimumab (Humira)   1TNF_ABC TNFalpha   0.93 2328 Complex Trimer Created
info 4DN4_LH:M AA 4DN3_LH CNTO888 FAB   1DOL_A MCP-1   0.81 1317
info 4FP8_HL:A AA 4FNL_HL C05   4FNK_ABCDEF influenza H3 HA   0.34 1322
info 4FQI_HL:ABEFCD AA 4FQH_HL CR9114 FAB   2FK0_ABCDEF H5N1 influenza virus hemagglutinin   1.08 1459 Complex Ligand Hexamer Created
info 4G6J_HL:A AA 4G5Z_HL Canakinumab antibody fragment   4I1B_A Interleukin-1 beta   0.61 1893
info 4G6M_HL:A AA 4G6K_HL Gevokizumab antibody fragment   4I1B_A Interleukin-1 beta   0.49 1673
info 4GXU_MN:ABEFCD AA 4GXV_HL 1F1 antibody   1RUZ_HIJKLM 1918 H1 Hemagglutinin   0.78 1830
info 4M5Z_HL:A AA 4M5Y_HL 5J8   3UYX_A influenza H1N1 HA1   0.73 1591
info 4Y7M_A:C AS 4QGY_A nb25   4Y7L_A E coli TssM CTD   0.84 1103
info 5GRJ_HL:A AA 4NKI_HL avelumab scFv (Bavencio)   4Z18_A PD-L1   1.14 1753
info 5JMO_D:B AS 5JMR_A Nb14   5JXI_A Furin   0.29 1394
info 5O14_HL:A AA 5UR8_AB 1A12   3KVD_D Neisseria meningitidis fHbp   0.63 1524
info 5O1R_HL:A AA 5NYX_HL 5H2   6CUJ_A Neisseria meningitidis NHBA   0.90 1852
info 5SV3_C:D AS 5SV4_A A3C8   1IFT_A Ricin   0.57 1294
info 5WK3_WV:D AA 5WK2_HL M116   1NR4_A CCL17   0.57 1222
info 5WUX_HL:EFG AA 5WUV_HL certolizumab (Cimzia)   1TNF_CBA TNFalpha   0.80 2073
info 5X0T_AB:E AA 5X4G_AB 6H8   3B5H_A CD147   1.25 1316
info 5Y9J_HL:ABC AA 5Y9K_HL belimumab (Benlysta)   1KXG_ABC B lymphocyte stimulator   0.96 1976 Complex Trimer Created
info 6A77_HL:A AA 6A76_HL B5209B   5O5I_A ROBO1 Ig5   0.95 1533
info 6B0S_HL:C AA 6B0W_HL 1710 Fab fragment   3VDJ_A circumsporozoite protein aTSR domain   0.72 1353
info 6BPC_EF:D AA 6BPB_AB 4F7   5W53_A Plasmodium vivax reticulocyte-binding protein 2b   0.47 1645
info 6CWG_B:A AS 6CWK_A A9   1IFT_A Ricin   0.76 1151
info 6DBG_C:B AS 6DBA_A R303   1H6T_A Listeria monocytogenes internalin B   0.46 1525
info 6OC3_AB:F AA 6OBZ_HL FluA-20   6CHX_A H1 hemagglutinin head   0.59 1537
info 1AVX_A:B EI 1QQU_A Porcine trypsin   1BA7_B Soybean trypsin inhibitor   0.47 1585
info 1AY7_A:B EI 1RGH_B RNase Sa   1A19_B Barstar   0.54 1237
info 1BUH_A:B EI 1HCL_ CDK2 kinase   1DKS_A Ckshs1   0.75 1324
info 1BVN_P:T EI 1PIG_ a-amylase   1HOE_ Tendamistat   0.87 2222
info 1CLV_A:I EI 1JAE_A a-amylase   1QFD_A(1) a-amylase inhibitor   0.86 2087
info 1D6R_A:I EI 2TGT_ Bovine trypsin   1K9B_A Bowman-Birk inhibitor   1.14 1408
info 1DFJ_E:I EI 9RSA_B Ribonuclease A   2BNH_ Rnase inhibitor ACE 1.02 2582
info 1E6E_A:B ES 1E1N_A Adrenoxin reductase FAD 1CJE_D Adrenoxin   0.96 2315
info 1EAW_A:B EI 1EAX_A Matriptase   9PTI_ BPTI   0.54 1866
info 1EWY_A:C ES 1GJR_A Ferredoxin reductase FAD 1CZP_A Ferredoxin   0.8 1502
info 1EZU_C:AB * EI 1TRM_A D102N Trypsin   1ECZ_AB Ecotin   1.21 2751
info 1F34_A:B EI 4PEP_ Porcine pepsin   1F32_A Ascaris inhibitor 3   0.93 3038
info 1F51_AB:E ER 1IXM_AB Sporulation response factor B   1SRR_C Sporulation response factor F   0.74 2407
info 1FLE_E:I EI 9EST_A Elastase   2REL_A(4) Elafin   1.02 1763
info 1GL1_A:I EI 1K2I_1 a-chymotrypsin   1PMC_A(6) Protease inhibitor LCMI II   1.21 1591
info 1GLA_G:F ER 1BU6_O Glycerol Kinase   1F3Z_A Glucose specific phosphocarrier   0.98 1304
info 1GXD_A:C EI 1CK7_A proMMP2 type IV collagenase   1BR9_A Metalloproteinase inhibitor 2   1.39 2445
info 1HIA_AB:I EI 2PKA_XY Kallikrein   1BX8_ Hirustatin   1.4 1737
info 1JTD_B:A EI 3QI0_A BLIP-II   1BTL_A TEM-1 beta-lactamase   0.44 2180
info 1JTG_B:A EI 3GMU_B Beta-lactamase inhibitor protein   1ZG4_A Beta-lactamase TEM-1   0.49 2600
info 1JWH_CD:A ER 3EED_AB Casein kinase II beta chain   3C13_A Casein kinase II a chain EMO 1.27 1452
info 1MAH_A:F EI 1J06_B Acetylcholinesterase   1FSC_ Fasciculin   0.61 2145
info 1OC0_A:B ER 1B3K_A Plasminogen activator inhibitor-1   2JQ8_A(4) Vitronectin Somatomedin B domain   1 1313
info 1OPH_A:B EI 1QLP_A a-1-antitrypsin   1UTQ_A Trypsinogen   1.21 1360
info 1OYV_A:I EI 1SCD_A Subtilisin Carlsberg   1PJU_A Two-headed tomato inhibitor-II   0.7 1930
info 1OYV_B:I EI 1SCD_A Subtilisin Carlsberg   1PJU_A Two-headed tomato inhibitor-II   0.47 1280
info 1PPE_E:I EI 1BTP_ Bovine trypsin   1LU0_A CMTI-1 squash inhibitor   0.44 1688
info 1R0R_E:I EI 1SCN_E Subtilisin carlsberg   2GKR_I OMTKY   0.45 1409
info 1TMQ_A:B EI 1JAE_ alpha-amylase 5HP 1B1U_A RAGI inhibitor   0.86 2401
info 1UDI_E:I EI 1UDH_ Uracyl-DNA glycosylase   2UGI_B Glycosylase inhibitor   0.9 2022
info 1US7_A:B ER 2FXS_A Heat shock protein 82 N-ter domain   2W0G_A HSP 90 co-chaperone CDC37 C-ter domain   1.06 1095
info 1WDW_BD:A ER 1V8Z_AB Tryptophan synthase beta chain 1   1GEQ_A Tryptophan synthase alpha chain   1.29 3148
info 1YVB_A:I EI 2GHU_A Falcipain 2   1CEW_I Cystatin   0.51 1743
info 1Z5Y_D:E ES 1L6P N-term of DsbD   2B1K_A E.coli CCMG protein   1.23 1346
info 2A1A_B:A ES 3UIU_A Eukayotic translation initiation factor 2-alpha kinase 2   1Q46_A eIF2 alpha subunit   1.35 1186
info 2A9K_A:B ES 1U90_A Ras-related protein Ral-A GDP 2C8B_X Mono-ADP-ribosyltransferase C3   0.85 1751
info 2ABZ_B:E EI 3I1U_A Carboxypeptidase A1   1ZFI_A(1) Leech carboxypeptidase inhibitor   0.9 1443
info 2AYO_A:B ER 2AYN_A Ubiquitin carboxyl-terminal hydrolase 14   2FCN_A Ubiquitin   1.39 3027
info 2B42_B:A EI 2DCY_A Xylanase   1T6E_X Xylanase inhibitor   0.72 2520
info 2GAF_D:A ER 3OWG_A Poly(A) polymerase VP55   1VPT_A Vaccinia protein VP39 MSE 0.69 3368
info 2J0T_A:D EI 966C_A MMP1 Intersitial collagenase   1D2B_A(20) Metalloproteinase inhibitor 1   1.23 1477
info 2MTA_HL:A ES 2BBK_JM Methylamine dehydrogenase   2RAC_A Amicyanin   0.41 1461
info 2O8V_A:B ES 1SUR_A PAPS reductase   2TRX_A Thioredoxin   1.37 1619
info 2OOB_A:B ES 2OOA_A Ubiquitin ligase   1YJ1_A Ubiquitin   0.85 808
info 2OOR_AB:C ER 1L7E_AB NAD(P) transhydrogenase subunit a part 1   1E3T_A NAD(P) transhydrogenase subunit beta NAP 1.42 2065
info 2OUL_A:B EI 3BPF_A Falcipain 2   2NNR_A Chagasin   0.53 1933
info 2PCC_A:B ES 1CCP_ Cyt C peroxidase HEM 1YCC_ Cytochrome C HEM 0.39 1141
info 2SIC_E:I EI 1SUP_ Subtilisin   3SSI_ Streptomyces subtilisin inhibitor   0.36 1617
info 2SNI_E:I EI 1UBN_A Subtilisin SOC 2CI2_I Chymotrypsin inhibitor 2   0.35 1628
info 2UUY_A:B EI 1HJ9_A Trypsin   2UUX_A Tryptase inhibitor from tick   0.43 1280
info 2YVJ_A:B ER 2YVF_A Ferredoxin reductase BPHA4 FAD,NAI,NAD 2E4P_A Biphenyl dioxygenase ferredoxin subunit FES 0.6 1377
info 3A4S_A:D EI 1A3S_A SUMO-conjugating enzyme UBC9   3A4R_A NFATC2-interacting protein SLD2 ubiquitin-like domain   0.72 1116
info 3K75_D:B ER 1BPB_A DNA polymerase beta   3K77_A Reduced XRCC1, N-terminal domain   0.64 1195
info 3LVK_AC:B ER 3LVM_AB Cysteine desulfurase IscS PLP 1DCJ_A(12) Sulfurtransferase tusA   0.81 1609 Complex Receptor Dimer Created
info 3PC8_A:C ER 3PC6_A DNA repair protein XRCC1   3PC7_A DNA ligase III-alpha BRCT domain MSE 0.5 1240
info 3SGQ_E:I EI 2QA9_E Streptogrisin B   2OVO_A Ovomucoid inhibitor third domain   0.39 1211
info 3VLB_A:B EI 3VLA_A EDGP   3VL8_A Xyloglucan-specific endo-beta-1,4-glucanase A   0.51 2020
info 4CPA_A:I EI 8CPA_A Carboxypeptidase A   1H20_A(9) Potato carboxypeptidase inhibitor   0.62 1175
info 4H03_A:B ES 1GIQ_A Iota toxin component IA NAD,NAI 1IJJ_A Alpha actin ATP 0.68 1474
info 4HX3_BD:A EI 4HWX_AB Neutral proteinase inhibitor ScNPI   1C7K_A Zinc endoprotease   0.9 2086 Receptor Dimer Created
info 7CEI_A:B EI 1UNK_D Colicin E7 nuclease   1M08_B Im7 immunity protein   0.7 1384
info 1A2K_C:AB OG 1QG4_A Ran GTPase GDP 1OUN_AB Nuclear transport factor 2   1.11 1603
info 1AK4_A:D OX 2CPL_ Cyclophilin   4J93_A HIV capsid   0.87 1029
info 1AKJ_AB:DE OX 2CLR_DE MHC class 1 HLA-A2   1CD8_AB T-cell CD8 coreceptor   1.14 1995 Ligand Dimer Created
info 1AZS_AB:C OG 1AB8_AB Adenylyl cyclase   1AZT_A AC activator Gs a complex GSP 0.72 1911
info 1E96_A:B OG 1MH1_ Rac GTPase GNP 1HH8_A p67 Phox   0.71 1179
info 1EFN_B:A OX 1AVV_A HIV-1-NEF protein   1G83_A SH3 domain   0.77 1254
info 1EXB_ABDC:EGFH OX 1QRQ_ABCD KV beta2 protein beta subunit NDP 1QDV_ABCD KV1.2 potassium channel N-terminal domain   0.62 3558 Complex Dimer of Tetramers Created
info 1FCC_AB:C OX 1FC1_AB Fc domain of IgG1 MO61   2IGG_A(3) Strep. protein G C2 fragment   0.93 1354
info 1FFW_A:B OX 3CHY_A Chemotaxis protein CheY   1FWP_A Chemotaxis protein CheA   1.43 1166
info 1FQJ_A:B OG 1TND_C Gt-alpha GSP 1FQI_A RGS9 MSE 0.91 1806
info 1GCQ_B:C OX 1GRI_B GRB2 C-ter SH3 domain   1GCP_B Vav N-ter SH3 domain   0.92 1208
info 1GHQ_A:B OR 1C3D_ Complement C3   1LY2_A Epstein-Barr virus receptor CR2   0.34 800
info 1GPW_A:B OX 1THF_D HISF protein   1K9V_F Amidotransferase HISH   0.65 2097
info 1H9D_A:B OX 1EAN_A Runx1 domain of CBFa1   1ILF_A(1) Dimerisation domain of CBF-beta   1.32 2121
info 1HCF_AB:X OR 1B98_AM Neurotrophin-4   1WWB_X TrkB-d5 growth factor receptor   0.88 2136
info 1HE1_C:A OG 1MH1_ Rac GTPase GNP 1HE9_A Pseudomonas toxin GAP dom. MES 0.93 2113
info 1I4D_D:AB OG 1MH1_ Rac GTPase GNP 1I49_AB Arfaptin   1.41 1657
info 1J2J_A:B OG 1O3Y_A Arf1 GTPase GTP 1OXZ_A GAT domain of GGA1   0.63 1209
info 1K74_AB:DE OR 1MZN_AB RXR-a   1ZGY_AB PPAR-gamma   0.8 2200
info 1KAC_A:B OR 1NOB_F Adenovirus fiber knob protein   1F5W_B Adenovirus receptor   0.95 1456
info 1KLU_AB:D OX 1H15_AB MHC class 2 HLA-DR1   1STE_ Staphylococcus enterotoxin C3   0.43 1254
info 1KTZ_A:B OR 1TGK_ TGF-beta   1M9Z_A TGF-beta receptor   0.39 989
info 1KXP_A:D OX 1IJJ_B Actin ATP 1KW2_B Vitamin D binding protein   1.12 3341
info 1M27_AB:C OX 1D4T_AB SAP-SLAM Complex   3UA6_A Fyn kinase SH3 domain   1.22 799
info 1ML0_AB:D OR 1MKF_AB Viral chemokine binding p. M3   1DOL_ Chemokine Mcp1   1.02 2069 Complex Receptor Dimer Created
info 1OFU_XY:A OX 1OFT_AB SulA (PA3008)   2VAW_A Cell division protein FtsZ GDP 1.1 1583
info 1PVH_A:B OR 1BQU_A IL6 receptor beta chain D2-D3 domains   1EMR_A Leukemia inhibitory factor   0.34 1403
info 1QA9_A:B OX 1HNF_ CD2   1CCZ_A CD58   0.73 1353
info 1RLB_ABCD:E OX 2PAB_ABCD Transthyretin   1HBP_ Retinol binding protein RTL 0.66 1439 Receptor Tetramer Created
info 1RV6_VW:X OR 1FZV_AB PIGF receptor binding domain   1QSZ_A Flt1 protein domain 2   1.09 1626
info 1S1Q_A:B OX 2F0R_A UEV domain   1YJ1_A Ubiquitin   0.98 1288
info 1SBB_A:B OR 1BEC_ T-cell receptor beta   1SE4_ Staphylococcus enterotoxin B   0.37 1064
info 1T6B_X:Y OR 1ACC_A Anthrax protective antigen   1SHU_X Anthrax toxin receptor   0.62 1948
info 1XD3_A:B OX 1UCH UCH-L3   1YJ1_A Ubiquitin   1.24 2281
info 1XU1_ABD:T OR 1U5Y_ABD TNF domain of APRIL   1XUT_A(11) TNF receptor superfamily member 13B TACI CRD2 domain   1.3 1697
info 1Z0K_A:B OG 2BME_A Rab4A GTPase GNP 1YZM_A RAB4 binding domain of Rabenosyn   0.53 1787
info 1ZHH_A:B OR 1JX6_A Autoinducer 2-binding periplasmic protein LuxP   2HJE_A Autoinducer 2 sensor kinase/phosphatase LuxQ   1.31 2189
info 1ZHI_A:B OX 1M4Z_A BAH domain of Orc1   1Z1A_A Sir Orc-interaction domain   0.68 1322
info 2A5T_A:B OX 1Y20_A NMDA receptor R1-4A subunit ligand-binding core   2A5S_A NMDA receptor R2A subunit ligand-binding core   1.28 1892
info 2AJF_A:E OR 1R42_A ACE2   2GHV_E SARS spike protein receptor binding domain   0.65 1704
info 2B4J_AB:C OX 1BIZ_AB Integrase (HIV-1)   1Z9E_A(1) PC4 and SFRS1 interacting protein   0.99 1273
info 2BTF_A:P OX 1IJJ_B Actin ATP 1PNE_ Profilin   0.75 2063
info 2FJU_B:A OG 2ZKM_X Phospolipase beta 2   1MH1_A Rac GTPase GNP 1.04 1245
info 2G77_A:B OG 1FKM_A GTPase-activating protein GYP1   1Z06_A Ras-related protein Rab-33B GNP 1.08 2524
info 2GTP_A:D OG 1GFI_A Alpha-1 subunit Guanine nucleotide-binding protein G(I) GDP 2BV1_A RGS1   0.54 1442
info 2HLE_A:B OR 2BBA_A Ephrin B4 receptor   1IKO_P Ephrin B2 ectodomain   1.4 2116
info 2HQS_A:H OX 1CRZ_A TolB   1OAP_A Pal   0.97 2333
info 2VDB_A:B OX 3CX9_A Serum albumin   2J5Y_A Peptostreptococcal albumin-binding protein   0.47 1798
info 2X9A_D:C OR 1S62_A(8) TolA C-terminal domain   2X9B_A G3P TolA binding domain   1.33 1571
info 3BIW_A:E OX 3BIX_A Neuroligin-1   2R1D_A Neuroligin-1-beta   0.39 1191
info 3BP8_AB:C OX 1Z6R_AB Mlc transcription regulator   3BP3_A PTS glucose-specific enzyme EIICB   0.45 1391
info 3D5S_A:C OX 1C3D_A Complement C3d fragment   2GOM_A Fibrinogen-binding protein C-ter domain   0.56 1620
info 3H2V_A:E OX 3MYI_A Vinculin tail domain   1WI6_A(8) Raver1 RRM1 domain   0.8 1263
info 3P57_AB:P OX 3KOV_AB MEF2A   3IO2_A p300 TAZ2 domain   0.53 1291
info 3P57_CD:P OX 3KOV_AB MEF2A   3IO2_A p300 TAZ2 domain   0.74 1177
info 3P57_IJ:P OX 3KOV_AB MEF2A   3IO2_A p300 TAZ2 domain   0.91 1126
info 4M76_A:B OR 1C3D_A C3D   1M1U_A Integrin alpha-M CD11B A-domain   0.43 1046
               
  Medium Difficulty (60)                
info 2DD8_HL:S AA 2G75_AB m396   2GHV_E SARS spike   2.19 1710
info 3EO1_AB:CF AA 3EO0_AB GC-1008 FAB fragment   1TGJ_AB Transforming Growth Factor-Beta 3   1.37 1630 Ligand Dimer Created
info 3G6D_LH:A AA 3G6A_LH CNTO607 FAB   1IK0_A(10) Interleukin-13   1.86 1793
info 3HI6_XY:B AA 3HI5_HL AL-57 FAB fragment   1MJN_A Integrin alpha-L I domain   1.65 1871
info 3L5W_LH:I AA 3L7E_LH C836 FAB   1IK0_A(11) Interleukin-13   0.48 1138
info 3RJQ_B:A AA 3R0M_A A12   3TGR_A C1086 HIV gp120   0.79 1734
info 3V6Z_AB:F AA 3V6F_AB FAB E6   3KXS_F Capsid protein assembly domain   1.83 1922
info 4ETQ_HL:C AA 4EBQ_HL LA5   4E9O_X vaccinia D8L IMV   0.47 2278
info 4M3K_B:A AS 4M3J_A cAb-H7S   4BLM_A B. licheniformis beta-lactamase   1.77 1588
info 4POU_B:A AS 4POY_A VHHmetal   6ETL_A bovine RNase A   1.83 1313
info 5CBA_AB:E AA 5C2B_HL 3B4 scFv   4ZAI_A CXCL13   1.49 1790
info 5E5M_B:A AS 5E03_A H11   5E56_A mouse CTLA-4   1.56 1341
info 5HGG_T:A AS 5HDO_A Nb4   4FUD_A uPA   0.84 1969
info 5HYS_CD:JK AA 2XA8_HL omalizumab (Xolair)   4GT7_AB IgE-Fc3-4   1.00 1332
info 5KOV_C:AB AA 5I30_HL PL-2 scFv   5KOU_AB astrovirus 2 capsid protein spike domain   1.69 1735
info 5VNW_D:A AS 5VNV_A Nb.b201   1E78_A human serum albumin   1.49 967
info 5WHK_HL:AB AA 5WHJ_HL DX-2507   5BXF_AB FcRn-B2M   1.88 1850
info 6A0Z_HL:A AA 6A0X_AB 13D4   2FK0_A H5N1 hemagglutinin head   1.28 1661
info 6AL0_HL:A AA 4YNY_AB NZ-1   6AKQ_A A. aeolicus site-2 protease homolog with PA tag insertion   1.89 1623
info 6EY6_I:AB AS 5FWO_A nb130   6EY5_AB P. gingivalis PorM   1.90 1807
info 1CGI_E:I EI 2CGA_B Bovine chymotrypsinogen   1HPT_ PSTI   2.02 2053
info 1IJK_A:BC ER 1AUQ_ Von Willebrand Factor dom. A1   1FVU_AB Botrocetin   0.68 1648
info 1JIW_P:I EI 1AKL_A Alkaline metalloproteinase   2RN4_A(1) Proteinase inhibitor   2.07 1997
info 1KKL_ABC:H ES 1JB1_ABC HPr kinase C-ter domain MSE 2HPR_ HPr   2.2 1641 Receptor Trimer Created
info 1M10_A:B ER 1AUQ_ Von willebrand factor dom. A1   1M0Z_B Glycoprotein IB-a   2.1 2097
info 1NW9_B:A ER 1JXQ_A Capase-9   2OPY_A BIR3-XPIA   1.97 2112
info 1R6Q_A:C ER 1R6C_X Clp protease subunit ClpA   2W9R_A Clp protease adaptor protein ClpS   1.67 1651
info 1ZM4_A:B ES 1N0V_C Elongation factor 2   1XK9_A Diphtheria toxin A catalytic domain   2.11 1554
info 2NZ8_A:B ER 1MH1_ Rac GTPase GNP 1NTY_A DH/PH domain of TRIO   2.13 2599
info 2Z0E_A:B ER 2D1I_A Cysteine protease Atg4B   1V49_A(1) Microtubule-associated proteins 1A/1B light chain 3B   2.15 2478
info 4FZA_A:B ER 1UPL_A MO25 alpha MSE 3GGF_A Serine/threonine-protein kinase MST4   2.04 1695
info 4IZ7_A:B EI 1ERK_A Non-phosphorylated ERK   2LS7_A(1) PEA-15 Death Effector Domain   1.56 1202
info 4LW4_AB:C ES 4LW2_AB Cysteine desulfurase CsdA PLP 1NI7_A(8) Cysteine desulfuration protein CsdE   1.6 1610 Receptor Dimer Created
info 1B6C_A:B OX 1D6O_A FKBP binding protein   1IAS_A TGFbeta receptor   1.96 1752
info 1FC2_C:D OX 1BDD_ Staphylococcus Protein A   1FC1_AB Human Fc fragment FUC,GAL,NAG,MAN 1.69 1307
info 1GP2_A:BG OG 1GIA_ Gi-alpha GSP 1TBG_DH Gi-beta,gamma   1.65 2287
info 1GRN_A:B * OG 1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP   1.22 2332
info 1HE8_B:A OG 821P_ Ras GTPase GTN 1E8Z_A PIP3 kinase   0.92 1305
info 1I2M_A:B OG 1QG4_A Ran GTPase GNP 1A12_A RCC1   2.12 2779
info 1IB1_AB:E OX 1QJB_AB 14-3-3 protein   1KUY_A Serotonin N-acteylase COT 2.09 2808
info 1K5D_AB:C OG 1RRP_AB Ran GTPase GNP 1YRG_B Ran GAP   1.19 2527
info 1LFD_B:A OG 5P21_A Ras GNP 1LXD_A RalGDS Ras-interacting domain   1.79 1167
info 1MQ8_A:B OX 1IAM_A ICAM-1 domain 1-2   1MQ9_A Integrin a-L I domain   1.76 1253
info 1N2C_ABCD:EF OX 3MIN_ABCD Nitrogenase Mo-Fe protein   2NIP_AB Nitrogenase Fe protein   2.13 3635
info 1SYX_A:B OX 1QGV_A Spliceosomal U5 15 kDa protein   1L2Z_A(1) CD2 receptor binding protein 2 C-ter fragment   1.64 1293
info 1WQ1_R:G * OG 6Q21_D Ras GTPase GCP 1WER_ Ras GAP   1.16 2913
info 1XQS_A:C OX 1XQR_A HspBP1   1S3X_A Hsp70 ATPase domain ATP 1.77 2350
info 2CFH_A:C OX 1SZ7_A BET3   2BJN_A TPC6   1.55 2384
info 2H7V_A:C OG 1MH1_ Rac GTPase GNP 2H7O_A YpkA   1.63 1574
info 2HRK_A:B OX 2HRA_A Glutamyl-t-RNA synthetase   2HQT_A GU-4 nucleic binding protein   2.03 1595
info 2OZA_B:A OX 3HEC_A MAP kinase 14   3FYK_X MAP kinase-activated protein kinase 2   1.89 6248
info 3AAA_AB:C OX 3AA7_AB Actin capping protein   1MYO_A(30) Myotrophin   1.78 1686
info 3AAD_A:D OX 1EQF_A Double bromodomain   1TEY_A(13) Histone chaperone ASF1   2 1461
info 3BX7_A:C OX 3BX8_A Lipocalin 2   3OSK_A CTLA-4 extracellular domain   1.63 2349
info 3CPH_G:A OG 3CPI_G Rab GDP-dissociation inhibitor   1G16_A Ras-related protein Sec4 GNP 2.12 1685
info 3DAW_A:B OX 1IJJ_A Alpha actin ATP 2HD7_A(5) Twinfilin-1 C-terminal domain   1.49 2323
info 3R9A_AC:B OR 1H0C_AB Alanine-glyoxylate aminotransferase PLP,LLP 2C0M_A PEX5P TPR repeat domain   1.91 1926 Receptor Dimer Created
info 3S9D_B:A OR 1N6U_A(15) IFNAR2   1ITF_A(9) IFNa2   1.69 1841
info 3SZK_DE:F OX 3ODQ_AB MetHaemoglobin HEM 2H3K_A ISDH-N1   2.1 1263
info 4JCV_ADBC:E OX 1VDD_ABCD Recombinational repair protein RecR   1W3S_A DNA repair protein RecO   1.62 1949
               
  Difficult (35)                
info 2FJG_HL:VW AA 2FJF_HL G6   4KZN_AB VEGF   2.51 1678 Ligand Dimer Created
info 4DW2_HL:U AA 4DVB_AB mAb-112   4DVA_U uPA   2.27 2038
info 5C7X_HL:A AA 5D7S_HL MOR04357   2GMF_A GM-CSF   2.31 2523
info 1ACB_E:I EI 2CGA_B Chymotrypsin   1EGL_ Eglin C   2.26 1544
info 1F6M_A:C ES 1CL0_A Thioredoxin reductse FAD 2TIR_A Thioredoxin 1   4.9 1821
info 1FQ1_A:B ES 1B39_A CDK2 kinase ATP,ACE 1FPZ_F CDK inhibitor 3   3.41 1832
info 1JK9_B:A ES 1QUP_A CCS metallochaperone   2JCW_A SOD1 superoxide dismutase   2.51 2130
info 1JMO_A:HL ER 1JMJ_A Heparin cofactor   2CN0_HL Thrombin   3.21 3461
info 1JZD_AB:C ER 1JZO_AB DsbC disurfide bond isomerase   1JPE_A DsbD disulfide bond isomerase   2.71 2026
info 1PXV_A:C EI 1X9Y_A Cystein protease   1NYC_A Cystein protease inhibitor   2.63 2336
info 1ZLI_A:B EI 1KWM_A Carboxypeptidase B   2JTO_A(6) Tick carboxypeptidase inhibitor   2.53 2084
info 2IDO_A:B ES 1J54_A DNA polymerase III e exonuclease domain   1SE7_A(1) HOT protein (P1 phage)   2.79 1953
info 2O3B_A:B EI 1ZM8_A NucA nuclease   1J57_A NuiA nuclease inhibitor   3.13 1675
info 2OT3_B:A ER 1YZU_A Rab21 GTPase GNP 1TXU_A Rabex-5 VPS9 domain   2.79 2306
info 3FN1_B:A ER 2EDI_A(5) UQ_con domain from NEDD8-conjugating enzyme UBE2F   2LQ7_A NEDD8-activaating enzyme E1 catalytic subunit MSE 3.65 1897
info 3H11_BC:A ER 4JJ7_AB Caspase-8 ASA,ACE,1MH,B3L,HLX,1U8 3H13_A c-FLIPL protease-like domain   3.79 3169
info 4GAM_AFBGCH:D ER 1XVB_ABCDEF Methane monooxygenase hydroxylase   1CKV_A(9) Methane monooxygenase regulatory protein B   5.79 6671
info 1ATN_A:D OX 1IJJ_B Actin ATP 3DNI_ Dnase I   3.28 1774
info 1BKD_R:S OG 1CTQ_A Ras GTPase 1GNP 2II0_A Son of sevenless   2.86 3163
info 1DE4_AB:CF OX 1A6Z_AB beta2-microglobulin   1CX8_AB Transferrin receptor ectodom.   2.59 2066
info 1E4K_AB:C OR 3AVE_AB FC fragment of human IgG 1 NAG,FUC,MAN 1FNL_A Human FCGR III   2.6 1634
info 1EER_A:BC OR 1BUY_A Erythropoietin   1ERN_AB EPO receptor   2.44 3347 Ligand Dimer Created
info 1FAK_HL:T OR 1QFK_HL Coagulation factor VIIa   1TFH_B Soluble tissue factor   6.18 3363
info 1H1V_A:G OX 1IJJ_B Actin ATP 1D0N_B Gelsolin   6.62 2071
info 1IBR_A:B OG 1QG4_A Ran GTPase GDP 1F59_A Importin beta   2.54 2270
info 1IRA_Y:X OR 1G0Y_R Interleukin-1 receptor   1ILR_1 Interleukin-1 receptor antagonist protein   8.38 3367
info 1R8S_A:E OG 1HUR_A Arf1 GTPase GDP 1R8M_E Sec 7 domain   3.73 2986
info 1RKE_A:B OX 1SYQ_A Vinculin head   3MYI_A Vinculin tail   4.25 2614
info 1Y64_A:B OX 2FXU_A Actin ATP 1UX5_A BNI1 protein   4.69 2745
info 2C0L_A:B OX 1FCH_A PTS1 and TRP region of PEX5   1C44_A SCP2   2.62 2013
info 2I9B_E:A OR 1YWH_A Urokinase plasminogen activator surface receptor   2I9A_A Urokinase-type plasminogen activator   3.79 2371
info 2J7P_A:D OX 1NG1_A SRP GTPase Ffh GDP 2IYL_D Cell division protein FtsY GDP 2.67 3008
info 3AAD_A:B OX 1EQF_A Double bromodomain   1TEY_A(4) Histone chaperone ASF1   4.37 1654
info 3F1P_A:B OX 1P97_A(9) HIF2 alpha C-terminal PAS domain   1X0O_A(5) ARNT C-terminal PAS domain   2.52 1919
info 3L89_ABC:M OR 3L88_ABC Ad21 fiber knob   1CKL_A CD46 SCR1 and SCR2 domains   2.51 2167
a Complex category labels:
EI = Enzyme-Inhibitor
ES = Enzyme-Substrate
ER = Enzyme complex with a regulatory or accessory chain
AA = Antibody-Antigen
AS = Antigen - Single domain Antibody
OG = Others, G-protein containing
OR = Others, Receptor containing
OX = Others, miscellaneous
b RMSD of Ca atoms of interface residues calculated after finding the best superposition of bound and unbound interfaces.
c Change in Accessible Surface Area upon complex formation calculated using NACCESS.
HETATMs column lists cofactors and small ligands present in the downloadable cleaned-up files.
We included those small molecules important for binding and other compounds on surfaces.
Glycosylations not crucial for binding were excluded.
Multimer column contains comments pertaining to any multimers created by symmetry prior to docking
if the asymmetric unit did not contain the full biologically relevant molecule.
* Cases marked with the asterisk are those that would be considered redundant under the SCOP Superfamily-Superfamily
pair non-redundancy criterion.
? Please follow the "+info" link for more information on those cases
The previous version of the Benchmark (5.0) can be found here.
The following Benchmark 5.0 cases were revised for Benchmark 5.5:
Antibody-Antigen complexes without unbound antibodies removed (were called AB)
1BVK removed
1BGX removed