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Table 1 Best rank for (re)scoring with ZDOCK, \(E_{86}^{\text {initial}}\), E 86, E OPEP, and \(E_{\text {OPEP}}^{\text {int}}\) for complexes from the ZDOCK benchmark 4.0. \(\varnothing \) indicates the average rank for the complex class in question

From: Evaluation of the coarse-grained OPEP force field for protein-protein docking

Complex ZDOCK \(E_{86}^{\text {initial}}\) E 86 E OPEP \(E_{\text {OPEP}}^{\text {int}}\)
Enzyme/inhibitor
1ACB 47 11 14 1 16
1AVX 1 128 3 27 31
1AY7 330 205 358 730 858
1BVN 1 39 1 98 1
1CGI 28 52 9 2 70
1CLV 1 2 1 1 1
1DFJ 1 102 1 14 4
1EAW 332 194 151 469 124
1EZU 121 919 11 946 559
1F34 176 428 2 1664 79
1FLE 1797 179 223 35 424
1GL1 49 116 8 107 34
1GXD 229 84 2 4 47
1HIA 389 88 901 1300 1392
1IJK 1296 924 355 70 5
1JIW 1350 504 553 989 851
1JTG 1 5 1 23 9
1MAH 1 80 87 9 27
1NW9 750 105 392 857 569
1N8O 11 11 14 9 12
1OC0 225 82 240 70 83
1OPH 28 150 422 903 822
2O8V 34 20 502 112 308
1OYV 3 34 1 2 381
1PPE 1 7 1 1 2
1R0R 533 896 40 151 856
1TMQ 7 228 3 295 1
1UDI 9 446 2 158 2
1YVB 11 86 47 220 67
2ABZ 689 670 772 619 1121
2B42 1 57 40 44 192
2J0T 1730 677 179 579 178
2MTA 1 122 104 13 43
2OUL 1 30 1 23 1
2SIC 1 145 1 3 5
3SGQ 309 158 16 596 260
2UUY 258 279 65 180 361
4CPA 1 1 4 1 20
7CEI 1 30 55 51 9
\(\varnothing \) 275.7 212.7 143.1 291.7 251.9
Antigen/antibody
1AHW 1387 542 1087 1161 1563
1BJ1 1 20 132 89 230
1BVK 10 143 356 6 283
1DQJ [a] 1671 150
1E6J 8 8 39 21 10
1FSK 5 5 181 135 373
1I9R 31 39 177 23 109
1IQD 2 41 1 4 1
1JPS 1261 221 14 1635 1930
1KXQ 6 192 34 532 9
1K4C 120 201 1077 14 166
1MLC 188 1194 104 395 314
1NCA 389 331 774 1091 1340
1VFB 45 163 198 33 586
2FD6 2 82 20 16 268
2HMI 62 178 516 4 766
2I25 12 2 7 45 39
2JEL 22 85 18 49 139
2VIS 725 557 1538 625 1095
\(\varnothing \) 313.0 246.1 435.4 414.6 485.3
Other complexes
1AKJ 754 47 1823 787 1887
1B6C 1 13 1 1 1
1BUH 62 25 304 10 2
1DE4 4 472 38 39 52
1F51 9 22 32 166 176
1FC2 1286 1672 1654 896 224
1FFW 41 47 47 111 433
1GLA 210 326 1013 329 1296
1GPW 3 2 1 111 997
1H9D 203 53 386 297 345
1HE1 821 1837 871 1907 1702
1I2M 354 828 3 482 262
1JK9 998 735 305 891 552
1JZD 31 141 208 3 92
1K74 1 26 1 110 717
1ML0 1 12 2 2 3
1RV6 1 188 4 1 2
1S1Q 1696 925 780 1635 932
1SYX 149 345 123 24 781
1T6B 439 224 14 130 30
1US7 150 107 772 283 341
1WDW 1 3 23 12 326
1XD3 3 25 1 1 1
1XU1 37 69 5 6 1
1Z5Y 31 1 1 1 1
1ZHI 187 43 608 156 471
2AJF 1115 318 1029 195 494
2A5T 824 421 148 573 1149
2AYO 6 112 3 700 902
2CFH 1 18 1 3 3
2HLE 54 29 20 52 74
2HRK 2 76 64 30 5
2IDO 171 314 73 577 11
2NZ8 1002 281 81 793 243
2VDB 43 36 1 13 309
2Z0E 123 181 187 684 1346
3BP8 998 375 131 538 242
3D5S 524 29 1 34 246
\(\varnothing \) 324.6 273.1 283.1 331.1 438.2
  1. [a] The rank is set to 2000 for calculating the average