Symmetric protein Docking Benchmark 1.0

@ Huang Lab

Click here to download the zipped benchmark package

Reference: Yan, Y, and Huang, S.-Y. A nonredundant benchmark for symmetric protein docking. 2018 to be submitted.

The benchmark dataset for symmetric protein docking(251 cases)


Bound strcuture Unbound structure Interface
PDB Chainsa Catb Symmetryc PDB chain Descriptiond Length rmsd(Å)e TM-socre HETATMs rmsd(Å)e fnatf
Easy (176 cases)
1E4M(1)_MM E C2 1W9D_M S. alba myrosinase 501 0.12 0.9998 0.09 100.00
1G8S(1)_AA O C2 1FBN_A fibrillarin homologue 230 0.14 0.9994 MSE 0.09 100.00
3C6X(1)_AA E C2 2YAS_A parvalbumin 257 0.10 0.9997 0.10 100.00
1JDW(1)_AA E C2 8JDW_A Glycine amidinotransferase 386 0.76 0.9908 0.11 94.32
1EA5(1)_AA E C2 2C5G_A Acetylcholinesterase 537 0.13 0.9997 0.14 100.00
1GQG(1)_AC E C2 1JUH_A quercetin 2,3-dioxygenase 350 0.33 0.9950 NAG BMA 0.15 96.48
1Z4M(1)_AA E C2 1Q92_A deoxyribonucleotidase 197 0.21 0.9933 0.17 97.30
2PSZ(1)_AB E C2 2PT0_A p38 MAP kinase 340 0.29 0.9984 OCS 0.18 93.02
1O1H(1)_AB E C2 5AVH_A Xylose isomerase 386 0.25 0.9987 0.21 97.31
2A9W(1)_AB E C2 1QQQ_A thymidylate synthase 264 0.26 0.9981 CME CXM 0.22 94.67
1GZC(1)_AA O C2 3N35_A lectin 242 0.42 0.9827 0.22 95.56
1ADL(1)_AA O C2 1G7N_A lipid binding protein 131 0.32 0.9946 0.24 94.44
1VPT(1)_AA E C2 4DCG_A methyltransferase VP39 307 0.21 0.9989 0.24 82.46
2H2N(1)_AB E C2 1S1D_A apyrase 331 0.25 0.9986 0.25 92.11
1J8U(1)_AA E C2 1PAH_A phenylalanine hydroxylase 308 0.31 0.9945 0.26 100.00
1OH0(1)_AB E C2 3SED_A Steroid Delta-isomerase 125 0.64 0.9815 CSD 0.27 93.83
1GE7(1)_AB E C2 1G12_A peptidyl-Lys metalloendopeptidase 167 0.47 0.9912 0.31 80.95
1NLR(1)_AA E C2 2NLR_A endoglucanase 234 0.42 0.9901 MHO 0.32 88.23
1R1D(1)_AB E C2 1TQH_A Carboxylesterase precursor 247 0.35 0.9634 MSE 0.33 96.77
1AAP(1)_AB I C2 1CA0_D protease inhibitor domain 54 0.38 0.9769 0.33 96.67
1THW(1)_AA O C2 2VHK_A Thaumatin-I 206 0.26 0.9976 0.33 92.31
4PRO(1)_AB E C2 2H5C_A alpha-lytic protease 198 0.36 0.9954 0.33 84.61
1NMS(1)_AB E C2 4JJE_A Caspase-3 257 0.38 0.9708 0.34 93.45
3DNI(1)_AA E C2 2A40_B Deoxyribonuclease-1 260 1.12 0.9762 0.34 84.21
1YZ3(1)_AB E C2 2G72_A PNMT 289 0.48 0.9909 0.34 82.35
1VKP(1)_AB E C2 3H7C_X Agmatine deiminase 383 0.34 0.9838 MSE 0.35 90.70
1IX1(1)_AB E C2 1N5N_A deformylase 180 0.36 0.9885 0.35 82.61
1JKX(1)_AB E C2 1CDE_A glycinamide ribonucleotide transformylase 212 0.86 0.9825 0.35 91.89
1MUN(1)_AA E C2 1KG2_A core fragment of MutY 225 0.42 0.9943 0.36 89.47
3CW9(1)_AB E C2 3CW8_X CoA ligase 504 9.77 0.8333 0.36 91.67
1XER(1)_AA O C2 2VKR_A ferredoxin 103 0.30 0.9839 MLZ 0.36 62.50
1FBT(1)_AB E C2 1C81_A Fructose-2,6-bisphosphatase 191 0.43 0.9672 MSE 0.37 96.55
2VL3(1)_AA E C2 4MMM_A Pdrx5 168 0.42 0.9923 0.37 96.23
1ZOE(1)_AA E C2 4RLK_A Casein kinase II subunit alpha 332 0.50 0.9882 0.38 93.55
3TLI(1)_AA E C2 4N4E_E Thermolysin 316 0.34 0.9973 0.38 100.00
2O99(1)_AD O C2 1TD5_A Acetate operon repressor 202 0.90 0.9453 MSE 0.38 82.14
2SAK(1)_AA E C2 1C76_A Staphylokinase 136 0.55 0.9835 0.39 83.33
1OVA(1)_AB O C2 1UHG_A Ovalbumin 385 0.38 0.9971 ACE SEP 0.40 89.02
1AMP(1)_AA E C2 1RTQ_A Aminopeptidase 299 0.26 0.9984 0.43 93.33
2GJ4(1)_AA E C2 4YI3_A Glycogen phosphorylase, muscle form 843 0.44 0.9943 2TH 0.43 92.45
2UZQ(1)_AB E C2 1QB0_A Cdc25B catalytic domain 211 1.19 0.9436 0.43 86.96
1GX5(1)_AA E C2 2WCX_A RNA Polymerase 537 0.60 0.9715 MSE 0.43 90.14
1GWL(1)_AA O C2 1W8U_A CBM29-2 149 0.27 0.9894 0.43 76.92
1LLF(1)_AB E C2 1CLE_A cholesterol esterase 534 0.29 0.9988 0.43 100.00
1JYA(1)_AB O C2 1L2W_B YopE regulator 123 0.50 0.9683 MSE 0.46 94.25
2IPR(1)_AB T C2 3QK2_A Large T antigen 134 0.79 0.9336 CME 0.47 82.35
1MQI(1)_AA M C2 4YU0_A Peptidyl-prolyl cis-trans isomerase A 263 0.86 0.9806 0.48 100.00
1XG7(1)_AB O C2 4PII_A hypothetical protein PF0907 250 0.52 0.9922 0.48 74.24
1JD0(1)_AB E C2 4HT2_A Carbonic anhydrase 12 263 0.45 0.9907 0.49 93.06
3VUB(1)_AA O C2 3HPW_A Cytotoxic protein ccdB 101 0.73 0.9682 0.50 92.68
1C3R(1)_AB E C2 1C3P_A HDAC homolog 375 0.39 0.9970 0.51 75.00
1WWS(1)_AB O C2 1WWI_A TGS domain of Threonyl-tRNA synthetase 148 0.69 0.9720 MSE 0.51 91.95
1I4J(1)_AB O C2 1BXE_A ribosomal protein L22 113 2.96 0.8728 MSE 0.51 80.00
1RG0(1)_AB O C2 1QVE_A Fimbrial protein 126 0.27 0.9957 0.54 62.50
2HRC(1)_AB E C2 2QD1_A Ferrochelatase 359 1.14 0.9775 0.55 77.69
1WC9(1)_AA T C2 2J3W_D trafficking protein particle complex subunit 3 182 0.77 0.9721 0.57 80.19
1BV1(1)_AA Ag C2 4BK7_A Birch Pollen Allergen Bet v 1 159 0.79 0.9759 0.58 83.64
1RCM(1)_AB E C2 2VB1_A Lysozyme C 129 0.80 0.9705 0.58 94.87
1CKU(1)_AB O C2 1B0Y_A HIPIP 85 0.63 0.9763 0.58 83.87
1WHO(1)_AA Ag C2 2VXQ_A pollen allergen Phl p 2 96 0.52 0.9792 0.58 74.07
1UW1(1)_AA O C2 3DGL_A synthetic protein 81 0.53 0.9431 0.58 95.75
1D1M(1)_BA O C2 1ORC_A Cro repressor 71 0.80 0.9148 0.59 71.43
1VI6(1)_AB O C2 1VI5_A 30S ribosomal protein S2P 208 0.49 0.9666 MSE 0.60 78.46
1W5R(1)_AB E C2 1GX3_A transferase 284 0.51 0.9835 0.60 75.00
1EDT(1)_AA E C2 1C8X_A Endo-Beta-N-Acetylglucosaminidase H 265 0.59 0.9913 0.61 74.60
1DTO(1)_AA O C2 2NNU_A Regulatory protein E2 205 0.67 0.9761 0.61 62.50
1HFS(1)_AA E C2 1HY7_A stromelysin-1 173 0.52 0.9400 0.62 63.33
1T3C(1)_AB O C2 3D3X_A Type E botulinum toxin 427 0.39 0.9974 0.63 75.61
1C9O(1)_AB O C2 1HZB_A cold shock proteins CspB 66 0.53 0.9709 0.65 52.00
1CLX(1)_AB E C2 1W32_A xylanase(Xyn10A) 348 0.42 0.9937 0.65 81.82
1BSL(1)_AB E C2 1LUC_B luciferase 324 0.69 0.9900 0.66 86.43
5P21(1)_AA E C2 2CE2_X GTPAase HRAS 166 1.68 0.9395 0.67 62.07
1BKF(1)_AA O C2 2PPN_A FKBP12 107 0.59 0.9776 FK5 0.67 65.31
1NCO(1)_AB O C2 1NOA_A apo-neocarzinostatin 113 0.47 0.9862 0.67 88.00
1VH4(1)_AB O C2 5AWF_B SufD 423 0.59 0.9843 0.68 86.09
2ZTA(1)_AB O C2 1RB5_C GCN4-Leucine 34 0.79 0.8052 ACE 0.68 80.85
1DJT(1)_AB O C2 1ZVG_A Alpha-like neurotoxin BmK-I 66 0.65 0.9289 0.69 61.77
1I58(1)_AB E C2 1I59_A histidine kinase CheA 189 0.78 0.9783 0.70 89.13
1WSW(1)_AA O C2 1F4P_A flavodoxin 147 0.49 0.9902 0.71 76.47
1OKH(1)_AB O C2 1ED0_A viscotoxin A3 46 0.88 0.8651 0.71 94.44
1BC2(1)_AB E C2 4C1H_A beta-lactamase 227 0.44 0.9714 0.72 95.00
1FVK(1)_AB M C2 4ZIJ_A DsbA 188 0.82 0.9844 0.73 73.91
1ES9(1)_AA E C2 3DT8_A Acetylhydrolase 232 0.46 0.9951 SGB 0.73 95.89
1A3A(1)_AC E C2 1J6T_A IIA(Mtl) 148 0.75 0.9751 0.77 78.95
1YPT(1)_AB E C2 4YAA_A Tyrosine Phosphatase YopH 306 0.58 0.9775 0.77 66.67
1IAZ(1)_AB O C2 1TZQ_A Equinatoxin II 175 0.54 0.9893 0.83 88.46
2WEA(1)_AA E C2 1BXO_A penicillopepsin 323 0.50 0.9947 0.84 62.50
1QKD(1)_AB O C2 1NXB_A neurotoxin B 62 0.99 0.9073 0.86 89.47
2IIM(1)_AA E C2 1H92_A SH3 domain of Lck 63 1.74 0.8413 0.90 75.00
8RSA(1)_AB E C2 1DY5_A Ribonuclease A 124 0.69 0.9815 IAS 0.91 71.19
1VLS(1)_AA O C2 1JMW_A Rmethyl-accepting chemotaxis protein II 146 0.95 0.9647 0.92 69.23
1EVX(1)_AB E C2 1A73_A INTRON 3 (I-PPO) ENCODED ENDONUCLEASE 163 1.05 0.9602 0.93 89.59
1BAM(1)_AA E C2 3BAM_A restriction endonuclease BamHI 213 6.07 0.8383 0.97 78.05
1YPQ(1)_AB M C2 3VLG_A LOX-1 CTLD 145 0.57 0.9834 0.98 46.30
1UQ5(1)_AA O C2 3PX8_X Preproricin 258 0.67 0.9859 1.01 93.75
1Q8R(1)_AB E C2 2H8C_A RusA Holliday junction resolvase 120 1.08 0.9422 1.01 74.47
2DUC(1)_AB E C2 5C5O_A 3C-like proteinase 306 1.30 0.9651 1.02 82.86
1BTK(1)_AB E C2 2Z0P_A Tyrosine kinase BTK 169 1.61 0.9551 1.02 84.38
1GY6(1)_AB O C2 1A2K_A NTF2 127 1.14 0.9650 1.04 84.27
1RZL(1)_AA O C2 1BV2_A lipid transfer protein 91 1.28 0.8934 1.04 70.27
2AIB(1)_AB O C2 1LJP_A beta-Cinnamomin Elicitin 98 0.70 0.9701 1.05 63.64
1SWV(1)_AB E C2 1RDF_A phosphonoacetaldehyde hydrolase 267 3.22 0.8274 1.08 77.50
1OB9(1)_AA E C2 1OB8_A Holliday Junction Resolving Enzyme 135 0.89 0.9697 1.09 84.21
1ECY(1)_AA I C2 1N8O_E ecotin 142 1.38 0.9294 BGC GLC 1.11 62.16
1CEI(1)_AA Ab C2 1UNK_A ColE7 87 1.22 0.9023 1.11 90.91
1SE8(1)_AA O C2 3UDG_B ssDNA binding protein 301 1.19 0.9039 MSE 1.13 66.67
1C02(1)_AB E C2 2R25_A YPD1 167 1.28 0.9607 1.15 64.71
3EIP(1)_AB I C2 2B5U_B Colicin E3 immunity protein 84 0.77 0.9611 1.16 68.00
1WHI(1)_AA O C2 487D_M 50S L14 ribosomal protein 122 1.07 0.9379 1.20 72.97
1GPR(1)_AA E C2 1AX3_A glucose permease IIA domain 162 3.99 0.8511 1.21 56.10
1Q08(1)_AB O C2 1Q0A_A Zn(II)-responsive regulator of zntA 99 1.25 0.8992 1.22 93.68
1EAJ(1)_AB O C2 2WBW_B CAR D1 128 1.27 0.9417 1.28 63.04
2BAY(1)_AD E C2 1N87_A U-box of Prp19 56 1.63 0.7908 1.35 78.12
1T1V(1)_AB O C2 1SJ6_A SH3BGRL3 101 2.06 0.8145 1.35 69.44
2OYN(1)_AA O C2 2VBU_A Riboflavin kinase 136 0.83 0.9706 1.37 50.00
1THF(1)_DD E C2 2A0N_A phosphate synthase subunit hisF 265 1.07 0.9747 1.43 60.00
4CPV(1)_AA O C2 1B8L_A parvalbumin 108 1.22 0.9361 ACE 1.44 70.37
2C9V(1)_AF E C2 1MFM_A SOD 153 0.96 0.9697 1.46 86.28
1CYW(1)_AA O C2 1CYX_A CyoA 205 0.89 0.9763 1.47 65.71
5HPG(1)_AB E C2 2KNF_A Plasminogen 86 1.31 0.8743 1.48 42.22
2SCP(1)_AB O C2 1Q80_A sarcoplasmic calcium binding protein 174 1.60 0.9134 1.49 75.39
1CMB(1)_AB O C2 1MJO_A Met repressor 104 2.27 0.8934 1.50 79.85
1IRO(1)_AAA O C3 1SMM_A Rubredoxin 54 0.17 0.9767 0.17 100.00
2IE7(1)_AAA O C3 2RAN_A annexin V 316 0.51 0.9953 0.18 87.10
2J2J(1)_ABD O C3 2W9L_C fibre protein 197 0.30 0.9965 0.21 95.35
1BRT(1)_AAA E C3 1A8U_A chloroperoxidase T 277 0.34 0.9970 0.23 92.59
1UAE(1)_AAA E C3 3KQJ_A UDP-N-acetylglucosamine 419 0.28 0.9962 IAS 0.34 67.50
1F3G(1)_AAA M C3 4JBW_M phosphotransferase IIA component 172 0.49 0.9884 0.48 81.82
1IJ2(1)_ABC O C3 1RB6_C GCN4 34 0.40 0.8984 ACE 0.55 73.68
2CRO(1)_AAA O C3 3CRO_L CRO 71 0.99 0.9365 0.59 66.67
1M0M(1)_AAA M C3 4Y9H_A Bacteriorhodopsin 226 0.62 0.9664 LI1 0.65 86.84
2PNK(1)_ABC E C3 3HK9_A Uronate isomerase 427 0.59 0.9560 MSE 0.70 86.92
1A12(1)_ABC O C3 1I2M_B RCC1 402 1.13 0.9837 0.72 74.51
1CBQ(1)_AAA T C3 2G7B_A retinoic acid-binding protein 2 137 0.80 0.9700 1.00 52.38
1K4M(1)_ABC E C3 1K4K_A Nicotinic acid mononucleotide adenylyltransferase 213 1.46 0.9543 1.23 73.91
1N2M(1)_ABC E C3 2QQD_C PvlArgDC 166 1.17 0.9701 1.28 85.53
1F8D(1)_AAAA E C4 1XOE_A Neuraminidase 387 0.17 0.9995 NAG MAN 0.13 99.06
2P7T(1)_CCCC M C4 4MSW_C pH-gated potassium channel KcsA 103 0.20 0.9938 IEM 0.31 96.61
6Q21(1)_ABCD E C4 2CE2_X GTPAase HRAS 166 1.82 0.9315 0.87 73.68
3CHB(1)_DEFGH O C5 5ELB_A Cholera enterotoxin B subunit 103 0.29 0.9948 0.23 93.48
1VPS(1)_ABCDE O C5 1CN3_A coat protein VP1 283 0.36 0.9967 0.28 96.51
2HEX(1)_ABCDE I C5 5PTI_A trypsin inhibitor 58 0.41 0.9418 0.41 86.36
2A3Y(1)_ABCDE O C5 3D5O_A Serum amyloid P-component 204 0.56 0.9914 0.63 92.45
1KQ1(1)_ABHIKM O C6 3QSU_A RNA chaperone Hfq 77 0.50 0.9668 0.45 86.28
2BW9(1)_MMMMMM T C6 1A6M_A myoglobin 151 0.47 0.9897 0.49 73.08
2CI2(1)_IIIIII I C6 2SNI_I chymotrypsin inhibitor 2 83 0.46 0.9743 0.50 69.05
1U7K(1)_ABCDEF O C6 2Y4Z_A capsid protein P30 140 0.59 0.9386 MSE 0.92 63.16
1OIH(1)_ABCD E D2 1OIJ_A putative Alkylsulfatase Atsk 301 0.18 0.9990 0.15 89.19
1UWS(1)_ABAB E D2 4EAM_A Beta-galactosidase 489 0.21 0.9992 0.18 96.61
2AIO(1)_AAAA E D2 5EVK_A Metallo-beta-lactamase L1 271 0.16 0.9993 0.19 92.22
2GLK(1)_AAAA E D2 5AVH_A Xylose isomerase 386 0.20 0.9992 0.23 95.96
1RIS(1)_AAAA O D2 1CQM_A ribosomal protein S6 101 0.28 0.9841 0.23 93.10
1L7L(1)_AAAA O D2 4LJH_A PA-I galactophilic lectin 122 0.20 0.9977 0.26 100.00
2FPZ(1)_ABCD E D2 5F03_A Tryptase alpha/beta-1 245 0.41 0.9951 0.28 82.67
1GZ5(1)_ABCD E D2 1UQU_A Trehalose-6-phosphate 482 1.32 0.9706 MSE 0.33 100.00
2FM0(1)_ABCD E D2 1Y2K_A Phosphodiesterase 4D I 349 0.58 0.9927 0.62 81.48
1GR7(1)_ABCD O D2 3U25_A Azurin 127 0.65 0.9727 CSO 0.78 76.92
2BO4(1)_ABEF E D2 2Y4K_A Mannosylglycerate Synthase 382 0.57 0.9942 0.82 62.26
1LU0(1)_ABAB I D2 2STA_I trypsin inhibitor 29 0.61 0.8887 0.82 75.00
2UU8(1)_AAAA O D2 2OVU_A Canavalia gladiata lectin 237 0.74 0.9856 0.97 57.14
1F41(1)_ABAB T D2 3I9A_A Transthyretin 127 0.54 0.9822 1.00 88.06
1HCJ(2)_BCBC O D2 2WUR_A GFP 238 0.77 0.9846 ABA GYS 1.46 72.73
1FS5(1)_ABABAB E D3 2WU1_A Glucosamine-6-Phosphate Deaminase 266 0.35 0.9971 16G 0.17 97.78
1UTT(1)_AAAAAA E D3 1Y93_A Macrophage metalloelastase 159 0.55 0.9867 CP8 0.53 79.31
1W92(1)_AAAAAA T D3 1Q1F_A Neuroglobin 151 0.53 0.9735 0.56 86.21
2H7C(1)_ABCDEF E D3 5A7G_A Carboxylesterase 1 532 0.64 0.9943 0.72 70.37
1F6R(1)_ABCDEF O D3 1F6S_A alpha-lactalbumin 123 0.73 0.9741 0.97 75.76
2HMT(1)_ABABABAB T D4 1LSU_A Conserved hypothetical protein yuaA 147 0.74 0.9821 NAI 0.61 60.61
2VUB(1)_ABCDEFGH O D4 3HPW_A Cytotoxic protein ccdB 101 0.83 0.9626 1.12 78.79
1QNU(1)_ABCDEABCDE O D5 1DM0_B Shiga toxin B subunit 69 0.30 0.9892 0.27 100.00
1COA(1)_IIIIIIIIIIII I D6 5FFN_I Subtilisin-chymotrypsin inhibitor-2A 72 0.62 0.9563 0.71 60.00
1ZNN(1)_ABCDEFABCDEF E D6 4WY0_A PdxS 305 1.03 0.9788 L5P 1.42 79.71
2FUF(1)_AAAAAA Ag H 2ITL_A large T antigen 133 0.97 0.9450 MSE 1.17 57.14
2CC6(1)_AAAAAAAAAAAA O T 2CCB_A Dodecin 68 0.09 0.9989 LUM 0.09 97.50
1H05(1)_AAAAAAAAAAAA E T 2Y71_A 3-dehydroquinate dehydratase 146 0.47 0.9845 0.40 97.30
2G9T(1)_ABCDEFGHIJKL O T 3R24_B nsp 10 155 0.58 0.9568 0.65 81.25
Medium (37 cases)
1YCC(1)_AA O C2 4N0K_A Cytochrome c iso-1 108 0.88 0.9694 1.53 33.33
1EV7(1)_AB E C2 1IAW_A TYPE II RESTRICTION ENZYME NAEI 317 3.37 0.7927 1.55 48.75
2J80(1)_AB E C2 1P0Z_A Sensor kinase citA 131 1.28 0.9075 MSE 1.57 68.18
1VC1(1)_AB O C2 1T6R_A Putative anti-sigma factor antagonist TM1442 110 1.73 0.8760 SEP 1.58 44.83
1M1F(1)_AB O C2 2C06_B Kid toxin protein 110 1.66 0.8620 1.60 76.34
2NYR(1)_AB E C2 5BWL_A SIRT5 290 0.91 0.9500 SVR 1.69 57.90
1ALU(1)_AA O C2 4J4L_C Interleukin-6 168 1.23 0.9472 1.70 59.26
2REZ(1)_AA E C2 3TVQ_A TCM Aro/Cyc 169 1.34 0.9518 1.73 56.36
1VP6(1)_AC M C2 4MUV_B Cyclic nucleotide-gated potassium channel mll3241 142 1.14 0.9207 1.76 66.67
1O6A(1)_AB O C2 1YAB_A flagellar rotor protein 87 2.12 0.8413 MSE 1.76 88.11
1LFA(1)_AB M C2 1MJN_A Integrin alpha-L 179 1.95 0.9379 1.79 87.50
1AA7(1)_AB O C2 1EA3_A Matrix protein M1 164 1.38 0.9425 1.80 52.05
1MML(1)_AA E C2 4XPC_A reverse transcriptase 259 1.29 0.9480 1.84 61.80
1BK5(1)_AB T C2 1EE4_A karyopherin alpha 423 1.65 0.9536 1.86 49.06
1UC2(1)_AB O C2 4DWR_A tRNA-splicing ligase RtcB 487 0.94 0.9849 1.92 49.27
1BM9(1)_AA O C2 1F4K_A replication termination protein 122 2.21 0.8739 1.93 87.62
1IPS(1)_AB E C2 1ODM_A Isopenicillin N synthase 331 1.35 0.9778 1.99 71.74
1M4Z(1)_AB O C2 1ZBX_A Origin recognition complex subunit 1 219 2.78 0.9241 2.07 83.33
1WTD(1)_AB E C2 1WTE_A EcoO109I 272 3.70 0.7995 2.09 72.97
1EZG(1)_AB O C2 1L1I_A Antifreeze Protein 84 2.21 0.7591 2.16 50.00
1MKK(1)_AB O C2 4GLS_E Vascular endothelial growth factor A 102 2.10 0.8399 2.18 87.91
1I4U(1)_AB T C2 1GKA_A crustacyanin A1 subunit 180 1.67 0.9588 2.33 76.83
1FD3(1)_AC O C2 1FQQ_A beta-defensin-2 41 2.45 0.5458 2.44 65.00
1QWT(1)_AB O C2 5JEL_A IRF-3 242 2.82 0.9277 2.50 60.00
1SG9(1)_AC E C2 1NV8_A hemK protein 284 1.65 0.9565 2.54 61.67
1QJH(1)_AA O C2 1FKA_F 30S ribosomal protein S6 101 1.89 0.8698 2.57 37.29
1BDO(1)_AA E C2 2BDO_A acetyl-CoA carboxylase 80 2.05 0.8289 2.64 47.06
1PFO(1)_AA O C2 1M3I_A perfringolysin O 471 2.99 0.8773 2.77 67.27
1DCS(1)_AAA E C3 1W28_A deacetoxycephalosporin C synthase 331 1.62 0.9259 2.05 61.70
1KHX(1)_AAA O C3 1DEV_A MAD homolog 2 196 2.09 0.9318 SEP 2.40 55.00
2P2L(1)_ABC O C3 1MH1_A rac 1 186 2.04 0.8850 GDP 2.57 40.00
1OVO(1)_ABAB I C4 3OVO_A Ovomucoid third domain cleaved RDI 56 2.31 0.8561 2.53 59.18
1NW2(1)_ABCD O D2 1RQM_A Thioredoxin 105 1.81 0.8587 1.72 60.61
1UJ2(1)_ABAB E D2 1UDW_A Uridine-cytidine kinase 2 252 1.52 0.9457 1.83 87.72
1OEC(1)_AAAA E D2 2PVF_A FGFR2 334 1.45 0.9420 PTR 2.01 45.45
1HDF(1)_ABAB O D2 1AG4_A spherulin 3a 103 2.10 0.7710 MSE 2.42 62.74
2MLT(1)_ABAB O D2 2MW6_A Melittin 27 1.61 0.4422 2.80 29.63
Difficult (38 cases)
1HRU(1)_AB E C2 2MX1_A Threonylcarbamoyl-AMP synthase 189 3.49 0.7483 MSE 3.03 52.00
1MSC(1)_AA O C2 2BU1_A MS2 coat protein 129 3.34 0.8564 3.24 71.32
1NQD(1)_AB E C2 1NQJ_B class 1 collagenase 119 7.28 0.8630 3.25 71.43
1KTJ(1)_AB Ag C2 1A9V_A mite allergen Der p 2 129 3.12 0.7544 3.32 27.66
1HN4(1)_AB E C2 2B00_A Phospholipase A2 124 2.01 0.9080 MJI 3.33 20.00
2PG2(1)_AB O C2 3ZCW_A Kinesin-like protein KIF11 348 3.70 0.8847 3.50 66.67
1K0Z(1)_AB E C2 3PVI_A PvuII endonuclease 157 2.44 0.8363 3.77 49.07
1DQZ(1)_AB Ag C2 4MQL_A Ag85C 304 2.85 0.9421 4.49 46.15
6INS(1)_EF O C2 1SJU_A proinsulin 50 5.77 0.5950 4.88 51.06
2GHV(1)_EC O C2 2GHW_A Spike glycoprotein 203 3.09 0.8458 5.24 58.11
1KCM(1)_AA T C2 1UW5_A Phosphatidylinositol Transfer Protein Alpha 270 3.79 0.8142 MSE 6.18 12.00
1D8H(1)_AB E C2 3KYH_A mRNA-capping enzyme subunit beta 310 11.10 0.9186 8.12 85.06
1ET1(1)_AB O C2 1ZWA_A Parathyroid hormone 34 9.01 0.3019 8.99 25.00
1USG(1)_AA T C2 1USI_A L-leucine-binding protein 346 7.14 0.6461 9.13 33.33
2GUD(1)_AB O C2 3LL2_A Griffithsin 123 9.62 0.8500 ACE 12.29 10.42
1MU4(1)_AB O C2 1K1C_A HPr-like protein, Crh 84 11.74 0.6301 13.29 2.58
1QB2(1)_AB O C2 1RY1_W SRP 54 kDa protein 109 11.96 0.6499 13.31 12.68
1DZ3(1)_AA O C2 1QMP_A Spo0A 130 9.14 0.7760 PHD 13.49 2.40
1HT9(1)_AB O C2 1IG5_A calbindin D9k 75 11.93 0.5407 13.54 11.63
1K51(1)_AA O C2 1HZ5_A B1 domain of PROTEIN L 72 13.04 0.7021 13.77 7.26
1M0D(1)_AB E C2 3CAE_A Endonuclease I 132 9.54 0.7354 14.93 7.66
1SND(2)_AB E C2 1SNC_A thermonuclease precursor 149 10.17 0.7730 15.23 17.20
1K04(1)_AA E C2 1OW6_B Focal adhesion kinase 1 161 13.92 0.7356 18.48 5.06
1UX5(1)_AA O C2 1Y64_B Actin 443 10.33 0.8523 19.70 5.04
1HW7(1)_AA O C2 3M7M_X hsp33 235 18.52 0.7384 24.38 13.13
1R4C(1)_AB I C2 3GAX_A Cystatin-C 120 19.16 0.5382 24.70 1.73
1I4M(1)_AA M C2 1H0L_A Prion Protein 112 21.39 0.5591 25.55 5.91
2CN4(1)_AB T C2 1DK0_A hemophore HasA 188 22.79 0.7276 27.05 2.15
1PM4(1)_ABC O C3 1POQ_A YPM 118 4.73 0.6872 4.50 52.50
1JS0(1)_ABC E C3 1DY5_A ribonuclease A 124 6.96 0.8886 IAS 7.96 14.81
1YVS(1)_AAA E C3 1A2P_A barnase 110 17.19 0.6579 18.00 9.78
3BKD(1)_EFGH M C4 1MP6_A Matrix protein M2 25 2.30 0.7436 MSE 3.08 17.65
7AHL(1)_ABCDEFG M C7 4YHD_D Alpha-hemolysin 302 17.03 0.8267 6.55 38.18
1RYW(1)_ABCD E D2 1EJD_A MurA 419 2.13 0.9551 IAS 3.96 55.36
2PI8(1)_ABCD E D2 2AE0_X MltA 345 3.92 0.7896 MSE 4.53 40.00
2QVU(1)_ABAB E D2 1NUW_A Fructose-1,6-bisphosphatase 337 5.01 0.9349 5.14 77.89
1G5Y(1)_ABCD O D2 1FM6_A RXRalpha 238 6.55 0.8345 10.80 7.14
1CKS(1)_ABCAB O D3 4Y72_C Cyclin-dependent kinases regulatory subunit 84 13.98 0.7618 15.88 0.73
a. The chains contained in the selected biological unit represented by the PDB code with its number in parenthesis(i.e.,1E4M(1)) of the bound structure.
b. Structure category labels: E=Enzyme, I=Inhibitor, M=Membrane protein, T=Transport protein, Ab=Antibody, Ag=Antigen, O=Others.
c. The symmetry type of the target.
d. The biological description of the unbound structure.
e. The rmsd is calculated based on Cα atoms after optimal superimposition of the bound and unbound structures.
 f. fnat is the fraction of native residue contacts of the superposed unbound structure.


huanglab@hust.edu.cn, Lab of Biophysics and Molecular Modeling