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Table 15 Comparison of Atomic Contact Energy for the Predicted Complexes and the Experimental Structures on Benchmark v4.0

From: Protein-protein binding site identification by enumerating the configurations

PDB E act a E pre b F r c F l d PDB E act E pre F r F l PDB E act E pre F r F l PDB E act E pre F r F l
2o8v(A:B) -96.7 -149.3 91.4 81.0 1a2k(C:B) -38.9 -314.8 72.7 71.8 2vis(B:C) 35.8 -389.7 62.8 61.1 1n2c(A:F) 97.6 -272.1 46.1 60.0
1hcf(A:X) -46.2 -13.4 90.9 83.7 4cpa(A:I) -47.6 -318.3 72.7 71.0 1acb(E:I) -157.4 -555.7 62.2 92.9 1xu1(A:T) 60.7 85.9 45.5 72.7
1z5y(D:E) -85.9 -51.1 89.7 90.0 1wq1(R:G) 161.0 306.0 72.4 77.3 1j2j(A:B) -49.1 -161.8 62.1 51.6 1gpw(A:B) 107.8 -144.5 45.0 75.7
1gcq(B:C) -5.3 4.4 88.9 94.1 1mah(A:F) -8.5 -303.0 72.4 64.3 1jzd(A:C) 55.2 78.5 61.6 57.1 1oyv(B:I) -70.5 -136.0 44.5 60.6
2j0t(A:D) -65.8 -74.5 88.9 93.3 1udi(E:I) 69.2 -93.0 72.0 50.0 2hmi(D:B) -7.1 -524.8 61.6 57.2 1d6r(A:I) 88.0 -66.6 43.4 66.7
1s1q(A:B) 20.4 168.1 88.2 90.9 1t6b(X:Y) 87.4 -675.9 71.9 54.2 1vfb(B:C) 81.7 191.4 61.5 59.3 2fju(B:A) 61.0 -658.9 43.1 27.9
2ayo(A:B) 340.9 384.2 86.8 96.3 2g77(A:B) 215.5 72.6 71.6 76.3 1b6c(A:B) -29.8 -130.3 61.1 47.6 2sic(E:I) -158.8 -321.2 42.9 74.1
1n8o(C:E) -91.8 -64.1 86.5 83.9 1wdw(B:A) 301.6 30.6 71.4 64.8 1oph(A:B) -10.1 -516.1 60.6 64.5 1eer(A:B) 143.2 219.2 42.1 71.4
1i4d(D:A) 30.0 -49.1 86.5 82.1 1jk9(B:A) 1.7 -150.6 71.4 69.9 1f51(A:E) 179.1 37.4 60.0 47.4 1ofu(X:A) -32.7 -193.5 41.8 62.9
1qa9(A:B) 260.0 -73.9 85.7 83.3 1gp2(A:B) 56.5 -48.6 71.4 72.7 2i25(N:L) 131.0 144.8 60.0 76.6 2abz(B:E) 34.0 -300.7 41.0 70.3
2hle(A:B) 83.0 179.3 85.3 95.2 1dqj(B:C) 119.4 104.1 71.4 71.4 1ktz(A:B) -24.0 -150.3 60.0 57.2 1fq1(A:B) 152.5 -187.8 40.8 30.8
1fle(E:I) -134.1 -248.0 84.6 96.5 1us7(A:B) 71.6 30.8 71.0 64.5 1i9r(H:A) 92.9 284.5 60.0 58.8 1jps(H:T) 258.6 366.2 37.8 66.7
1jtg(B:A) 232.8 257.6 84.4 86.1 1kkl(A:H) 105.2 -252.2 71.0 75.0 1sbb(A:B) 0.5 154.1 60.0 58.8 1xqs(A:C) 368.9 383.0 37.2 23.3
1hia(B:I) -4.8 51.3 83.7 56.0 3d5s(A:C) 89.8 -70.8 70.8 68.3 1ffw(A:B) 79.2 68.9 59.2 62.1 1zm4(A:B) 118.6 -236.7 35.8 33.3
1k5d(A:C) 197.6 305.1 81.5 79.5 1r6q(A:C) -71.5 -129.3 70.4 64.9 2i9b(E:A) 58.0 -87.2 59.0 76.5 1ijk(C:A) 85.1 -45.5 35.7 14.8
1yvb(A:I) -141.9 -271.2 80.8 72.2 1he1(C:A) 20.6 242.2 70.3 66.6 1pxv(A:C) 28.5 -79.4 58.8 76.2 1tmq(A:B) 2.1 -466.6 35.1 63.0
1fak(L:T) 108.7 217.2 80.0 75.6 1rv6(V:X) -17.7 -3.7 70.0 52.6 1r0r(E:I) -126.0 -127.4 58.8 61.5 2ido(A:B) -71.8 92.8 33.4 39.0
3sgq(E:I) -57.9 26.3 80.0 75.0 1bkd(R:S) 195.0 -49.0 69.6 78.6 1e6j(H:P) 14.9 -366.7 58.8 40.0 1oc0(A:B) 27.1 -417.1 33.3 66.7
1pvh(A:B) 121.5 13.5 80.0 62.9 1avx(A:B) 31.8 35.1 69.2 81.5 1jmo(A:H) -49.0 -492.6 57.9 32.5 1y64(A:B) 123.8 -239.0 32.3 36.0
2oob(A:B) -15.8 -28.9 80.0 78.3 1zhi(A:B) 93.8 -89.3 68.7 64.5 3cph(G:A) 84.4 -193.3 57.7 68.3 1dfj(E:I) 159.3 -394.3 32.1 44.4
1oyv(A:I) -152.8 -158.1 79.3 66.7 1kac(A:B) 92.6 66.9 68.6 57.9 1ewy(A:C) 55.6 -80.1 57.2 63.1 1m10(A:B) 168.3 -36.2 31.8 54.1
1i2m(A:B) 300.9 213.4 79.2 79.4 1gl1(A:I) -83.2 -282.7 68.1 78.8 2h7v(A:C) 67.5 9.9 57.2 73.2 1ira(Y:X) 212.7 48.1 31.8 25.0
1atn(A:D) -72.3 -365.5 79.1 73.3 1e6e(A:B) 246.8 -137.5 67.7 73.4 1qfw(M:B) 60.9 61.7 57.2 48.0 2oul(A:B) -123.9 -311.2 30.4 54.0
1klu(A:D) 60.2 -243.4 79.0 54.5 1bj1(H:W) 10.9 -139.6 66.7 71.0 2z0e(A:B) -38.7 -562.7 56.4 63.8 1k74(A:D) 127.4 145.5 30.0 27.3
2hrk(A:B) -5.4 -52.5 78.9 86.4 1k4c(A:C) 70.3 -216.1 66.7 52.2 2vdb(A:B) 77.4 -562.9 56.3 58.3 1ghq(A:B) -0.5 -175.5 30.0 42.1
1efn(B:A) 30.0 173.4 78.8 89.7 1fc2(C:D) 23.1 -93.1 66.7 70.6 1f6m(A:C) 14.6 -307.7 56.0 63.8 3bp8(A:C) 57.9 -429.9 30.0 53.0
1buh(A:B) 70.5 151.9 78.8 71.1 2jel(H:P) 74.0 18.2 66.7 75.9 1e4k(A:C) -41.5 -385.7 55.1 48.0 1azs(A:C) -65.7 -331.5 28.6 51.4
2sni(E:I) -125.0 -1.9 78.8 87.5 1zhh(A:B) -84.0 -537.9 66.7 64.3 1zli(A:B) -100.2 -164.6 54.1 52.4 1he8(B:A) 64.0 -323.3 27.4 40.0
1mlc(B:E) 74.4 -133.7 78.8 62.0 1gla(G:F) -26.3 -232.4 66.7 65.4 1kxp(A:D) 189.4 -311.2 54.0 54.8 2fd6(H:U) 78.6 -317.1 27.3 31.6
1qfw(H:A) 36.5 150.4 78.6 45.4 1ml0(A:D) -95.8 -641.1 66.7 60.4 1clv(A:I) 0.3 -648.0 54.0 79.1 1fqj(A:B) 234.8 326.9 26.4 25.9
1xd3(A:B) -5.2 -240.3 78.0 63.4 1z0k(A:B) 9.7 -84.1 66.6 80.0 1de4(A:C) 123.1 -535.6 54.0 49.3 1syx(A:B) 116.4 113.1 26.3 66.7
2mta(L:A) -55.7 70.5 77.4 80.0 2nz8(A:B) 52.1 36.3 66.6 77.1 1jiw(P:I) 110.3 -628.9 53.9 66.7 2b42(A:B) 103.6 -199.4 24.0 23.6
1nw9(B:A) -120.1 -333.9 77.3 80.0 1e96(A:B) 110.7 -120.4 66.6 60.6 2b4j(A:C) 94.0 -120.6 53.8 66.7 1eaw(A:B) 12.0 -173.1 23.2 74.3
2c0l(A:B) 130.2 -225.3 76.7 78.1 2oor(A:C) -50.4 -839.7 66.6 41.0 1ezu(C:B) -103.2 -172.2 53.1 66.7 2pcc(A:B) 47.3 98.9 22.2 30.3
1iqd(A:C) -14.3 -261.7 76.5 52.2 2ajf(A:E) 59.4 -194.7 64.8 57.1 1rlb(B:E) -69.1 -322.3 52.7 63.2 1gxd(A:C) 45.2 -680.4 21.9 72.1
1nsn(L:S) 73.6 122.8 76.2 38.7 1ahw(B:C) 262.7 388.1 64.7 80.0 1ibr(A:B) 234.0 -850.1 51.3 38.5 2j7p(A:D) 208.9 122.5 21.7 30.2
1nca(H:N) 146.6 78.6 75.9 66.6 1lfd(B:A) 85.3 -28.0 64.5 85.7 2ot3(B:A) -165.8 -494.1 51.1 52.4 1h1v(A:G) 115.0 -60.2 20.4 38.9
2z9k(A:B) 67.0 -89.9 75.6 83.3 1ay7(A:B) 123.2 -30.3 64.5 77.4 1cgi(E:I) -186.4 -383.8 51.0 80.0 2oza(B:A) 287.3 -5.2 20.2 39.1
1grn(A:B) 189.3 -80.6 75.6 66.7 2btf(A:P) 165.6 102.3 64.0 50.0 1akj(A:D) 108.3 11.1 51.0 61.6 1kxq(H:A) 63.7 -497.6 19.7 28.1
1bgx(L:T) 127.3 -727.9 75.3 59.5 1bvk(E:F) 76.8 150.6 64.0 46.1 1f34(A:B) -70.5 -376.9 49.3 66.6 1jwh(C:A) -27.8 -305.7 18.7 35.3
1ppe(E:I) -54.5 -6.3 75.0 72.8 1h9d(A:B) 12.9 167.7 63.6 72.4 1fsk(C:A) 60.7 -19.8 48.3 45.2 1bvn(P:T) -43.9 -785.8 18.5 65.1
2cfh(A:C) -162.0 -435.9 74.4 73.9 7cei(A:B) 216.5 192.5 63.2 68.8 1ak4(A:D) -48.6 60.8 47.1 56.0 2o3b(A:B) 119.0 -17.4 14.3 28.6
1fcc(A:C) 247.3 160.9 74.1 66.7 1wej(L:F) 117.5 48.0 63.2 50.0 1mq8(A:B) 40.7 -56.3 46.7 84.9 1r8s(A:E) 38.2 90.0 12.6 57.7
2uuy(A:B) -10.2 -127.7 73.5 86.9 1ib1(A:E) 163.1 240.4 62.8 63.4 2a5t(A:B) 107.0 -227.5 46.5 48.9 2hqs(A:H) 190.9 -202.6 10.5 22.6
  1. aE act is ACE score for the experimental structure on the data set.
  2. bE pre is ACE score for the prediction complex on the data set.
  3. cF r (%) is the F-score of our method for the receptor protein on the data set.
  4. dF l (%) is the F-score of our method for the ligand protein on the data set.