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. Author manuscript; available in PMC: 2015 Mar 23.
Published in final edited form as: J Comput Chem. 2013 May 21;34(20):1743–1758. doi: 10.1002/jcc.23304

Table 1.

Application of DOT to Benchmark 2.0

PDB Total in DOT 200,000 (best) DOT-> ASP+Eleca Number in top ACE+Elec -> ASP+Elecb Number in top ZDOCK Number in top
2,000 100 30 (best) 2,000 100 30 (best) 2,000 (best)
1ACB_b 379 (213) 16 12 8 (1) 376 36 15 (1)
1ACB_u (0 bumps) 15 (9480) 0 0 0 (–) 1 0 0 (1392) 0 (–)h
1ACB_u (10 bumps) 3 (103,429) 0 0 0 (–) 0 0 0 (–) 0 (–)
1AHW_b 1561 (2) 219 74 20 ( 3) 0 0 0 (–)
1AHW_u (0 bumps) 898 (33) 61 6 1 (19) 0 0 0 (–) CDRsc 24 (8)
1AHW_u (10 bumps) 965 (342) 16 6 0 ( 55) 0 0 0 (–)
1AK4_b 0 0 0 0 (–) 0 0 0 (–)
1AK4_u 0 0 0 0 (–) 0 0 0 (–) 0 (–)
1AKJ_bd 789 (1) 169 9 0 ( 33) 0 0 0 (–)
1AKJ_u 853 (34) 29 0 0 ( 178) 0 0 0 (–) 6 (40)
1AY7_b 2427 (1) 400 89 27 ( 1) 0 0 0 (–)
1AY7_u 492 (405) 5 3 2 ( 14) 0 0 0 (–) 24(111)
1B6C_b 339 (20) 39 39 30 ( 1) 139 100 30 ( 1)
1B6C_u 300 (572) 2 2 2 ( 3) 193 60 16 (4) 18(1)
1BJl_b 67 (4177) 0 0 0 (–) 61 55 15 (3)
1BJl_uUBBf (0 bumps) 4 (68,905) 0 0 0 (–) 3 3 3 ( 4) CDRs 61 (2)
1BVK_b 53 (15,955) 0 0 0 (–) 0 0 0 (–)
1BVK_u (0 bumps) 30 (24,205) 0 0 0 (–) 0 0 0 (–)
1BVK_u (10 bumps) 2 (162,117) 0 0 0 (–) 0 0 0 (–) CDRs 0 (3970)
1BVN_b 1208 (1) 222 96 28 ( 1) 91 80 29 ( 1)
1BVN_u 1551 (107) 48 40 24 ( 1) 53 19 2 ( 17) 48 (14)
1CGI_b 466 (1) 129 100 30 ( 1) 455 100 30 ( 1)
1CGI_u 175 (174) 6 3 2(5) 4 4 4(2) 11 (23)
1D6R_be 1064 (96) 59 0 0 ( 542) 0 0 0 (–)
1D6R_ue 3 (108,109) 0 0 0 (–) 0 0 0 (–) 2 (984)
1DFJ_b 200 (1) 175 98 30 ( 1) 0 0 0 (–)
1DFJ_u 832 (2) 289 93 29 ( 1) 0 0 0 (–) 73 (1)
1DQJ_b 113 (1428) 3 3 3 ( 10) 0 0 0 (–)
1DQJ_u 0 0 0 0 (–) 0 0 0 (–) CDRs 0 (2287)
1E6J_b 66 (30,300) 0 0 0 (–) 64 56 6 ( 23)
1E6J_u (0 bumps) 133 (6070) 0 0 0 (–) 86 26 1 ( 14) CDRs 121 (1)
1E6J_u (10 bumps) 0 0 0 0 (–) 0 0 0 (–)
1E96_be 177 (67) 3 0 0 ( 229) 17 0 0 ( 979)
1E96_ue 242 (39) 6 1 1 ( 21) 54 2 0 ( 42) 16 (16)
1EAW_bd 728 (1) 158 1 0 ( 100) 5 1 0 ( 90)
1EAW_ud 2820 (12) 125 0 0 ( 393) 6 0 0 ( 1516) 62 (3)
1F34_b 323 (1) 136 81 30 ( 1) 145 85 30 ( 1)
1F34_u 393 (63) 34 0 0 ( 117) 117 3 0 ( 74) 13 (5)
1FQl_b 402 (4) 44 40 25 (1) 19 12 5 (11)
1FQ1_u 0 0 0 0 (–) 0 0 0 (–) Not run
1FQJ_bd 747 (1) 130 0 0 ( 293) 0 0 0 (–)
1FQJ_u 42 (16,731) 0 0 0 (–) 0 0 0 (–) 0 (5551)
1FSK_b 293 (119) 13 13 13(1) 4 4 3(11)
1FSK_u UBB (0 bumps) 171 (399) 2 2 2 ( 4) 0 0 0 (–) CDRs 163 (1)
1GCQ_bd 319 (13) 29 1 0 ( 80) 0 0 0 (–)
1GCQ_u 0 0 0 0 (–) 0 0 0 (–) 1 (429)
1GP2_b 376 (1) 67 61 30 ( 1) 102 69 29 ( 1)
1GP2_ue 0 0 0 0 (–) 0 0 0 (–) 0 (–)
1GRN_bd,e 563 (1) 254 43 16(1) 30 16 8 ( 2)
1GRN_ue (0 bumps) 1118 (291) 32 0 0 ( 500) 0 0 0 (–) 6 (807)
1GRN_ue (10 bumps) 1244 (1425) 3 0 0 ( 1560) 0 0 0 (–)
1HEl_b 443 (1) 76 70 30 ( 1) 38 38 22 ( 1)
1HEl_ue 211 (735) 3 0 0 ( 158) 0 0 0 (–) 2 (258)
1HIA_b 1254 (22) 199 47 14 ( 4) 95 14 4 (2)
1HIA_ue 0 0 0 (–) 0 0 0 (–) 0 (–)
H2M_b 697 (1) 171 58 20 ( 1) 0 0 0 (–)
H2M_ue (0 bumps) 51 (694) 3 1 0 ( 37) 0 0 0 (–) 0 (34,162)
H2M_ue (10 bumps) 113 (11,749) 0 0 0 ( 0) 0 0 0 (–)
H9R_b 438 (113) 25 0 0 ( 106) 0 0 0 (–)
H9R_u UBB (0 bumps) 185 (151) 3 0 0 ( 166) 0 0 0 (–) CDRs 16 (20)
UPS_b 1738 (3) 308 73 16(1) 0 0 0 (–)
UPS_u (0 bumps) 1080 (40) 50 4 1 ( 7) 0 0 0 (–) CDRs 18 (53)
UPS_u (10 bumps) 880 (462) 6 0 0 ( 107) 0 0 0 (–)
1K5D_bd 394 (1) 105 0 0 ( 102) 43 0 0 ( 156)
1K5D_u (0 bumps) 47 (463) 2 0 0 ( 1668) 0 0 0 (–) 8 (134)
1K5D_u (10 bumps) 143 (10,317) 0 0 0 (–) 0 0 0 (–)
1KAC_b 864 (5) 59 10 3 ( 18) 0 0 0 (–)
1KAC_ud 409 (80) 9 0 0 ( 812) 0 0 0 (–) 3 (72)
1KTZ_b 1332(508) 18 0 0 ( 171) 64 20 2 ( 26)
1KTZ_u (0 bumps) 267 (4403) 0 0 0 (–) 76 1 0 ( 83) 7 (804)
1KTZ_u (10 bumps) 10 (118,002) 0 0 0 (–) 1 0 0 ( 513)
1KXP_b 277 (1) 142 93 30 ( 1) 20 18 13(1)
1KXP_ud,e 1635 (1) 316 39 10 (5) 17 1 0 ( 62) 20 (1)
1M10_b 844 (1) 144 39 6 ( 12) 94 1 1 ( 15)
1M10_ue 0 0 0 0 (–) 0 0 0 (–) 0 (–)
1MAH_be 1038 (1) 198 100 30 ( 1) 186 93 30 ( 1)
1MAH_ue 1151 (1957) 1 1 1 ( 1) 344 68 22 ( 1) 85 (1)
1MLC_b 223 (1668) 1 1 1 ( 4) 1 1 1 ( 10)
1MLC_u (0 bumps) 22 (26816) 0 0 0 (–) 3 2 0 ( 91) CDRs 39 (5)
1MLC_u (10 bumps) 0 0 0 0 (–) 0 0 0 (–)
1NCA_b 455 (8) 47 44 14 ( 10) 0 0 0 (–)
INCA_u UBB (0 bumps) 113 (616) 5 5 3 ( 9) 0 0 0 (–) CDRs 50 (4)
1PPE_b 1124 (3) 235 61 25 ( 1) 173 32 7(5)
1PPE_u 2327 (223) 37 33 8 ( 2) 508 94 29 ( 1) 324 (1)
1QA9_bd 1181 (1) 118 0 0 ( 174) 0 0 0 (–)
1QA9_u 0 0 0 0 (–) 0 0 0 (–) 2 (850)
1UDI_b 1583 (1) 317 96 29 ( 1) 71 11 5(1)
1UDI_u 1013 (8) 16 15 7(5) 6 1 1 ( 19) 7 (13)
1WEJ_b 723 (31) 31 31 27 ( 1) 0 0 0 (–)
1WEJ_u (0 bumps) 627 (114) 15 15 15(1) 0 0 0 (–) CDRs 55 (1)
1WEJ_u (10 bumps) 83 (25,317) 0 0 0 (–) 0 0 0 (–)
2BTF_b 672 (1) 141 91 28 ( 2) 0 0 0 (–)
2BTF_u (0 bumps) 260 (18) 12 7 4(1) 0 0 0 (–) 7 (96)
2BTF_u (10 bumps) 738 (299) 9 8 6 ( 7) 0 0 0 (–)
2MTA_b ETg 240 (489) 5 5 5(1) 136 56 23 ( 1)
2MTA_u ET (0 bumps) 11 (76,179) 0 0 0 (–) 1 0 0 ( 507) 1 (1722)
2PCC_b ET 1956 (9) 62 13 7 ( 7) 225 23 8 ( 7)
2PCC_u ETe (0 bumps) 476 (337) 2 0 0 ( 842) 0 0 0 (–) 1 (1037)
2SIC_b 98 (1440) 1 1 1 ( 26) 79 47 7 ( 7)
2SIC_u (0 bumps) 19 (8114) 0 0 0 (–) 14 5 4(5) 69 (1)
2SIC_u (10 bumps) 0 0 0 0 (–) 0 0 0 (–)
2SNI_b 262 (348) 12 12 12(1) 241 100 30 ( 1)
2SNI_u (10 bumps) 0 0 0 0 (–) 0 0 0 (–) 6 (300)
7CEI_bd 2151 (2) 166 4 0 ( 33) 0 0 0 (–)
7CEI_u 1652 (1) 81 13 5(2) 0 0 0(–) 186 (1)
a

The top 2,000 DOT configurations rescored by ASP+Elec. Note that the number in the top 2,000 corresponds to that found by DOT scoring.

b

The top 2,000 ACE+Elec configurations rescored by ASP+Elec.

c

CDRs: ZDOCK was restrained to the CDRs of the antibody and therefore ZDOCK results are not comparable to the unrestrained DOT runs.

d

The DOT score gave the best results for bound complexes [top 2,000, top 100, top 30 (best)] 1AKJ: 169, 46, 23 (1); lEAW_b: 158, 39, 18 (1); 1FQJ: 130, 27, 10 (1); 1GCQ: 29, 4, 3 (13); 1GRN: 254, 86, 30 (1); 1K5D: 105, 42, 25 (1); 1M10: 144, 31, 16 (1); 1QA9: 118, 28, 12 (1); 7CEI: 166, 28, 13 (2), and for unbound complexes 1EAW: 125, 10, 2 (12); 1KAC: 9, 1, 0 (80); 1KXP: 316, 43, 17(1).

e

Noninteger charge, multiple side chains incomplete.

f

UBB: Coordinates are of an unbound/bound system.

g

ET: An electron-transfer complex.

h

ZDOCK found no hits.