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Table 5 Detailed Results of DoBi, metaPPI, meta-PPISP and PPI-Pred on 41 complexes

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

Complex Protein 1 Protein 2
  PDBa Int n b DoBi metaPPIf meta-PPISPf PPI-Predg PDB Int n DoBi metaPPI meta-PPISP PPI-Pred
    Acc c Cov d Acc Cov Acc Cov Acc Cov    Acc Cov Acc Cov Acc Cov Acc Cov
E-Ie  
1acb(E:I)h 2cgaB 24 33.3 20.8 87.5 56.0 60.7 68.0 76.0 79.2 1egl_ 13 63.2 92.3 66.7 58.8 100 53.6 90.0 69.2
1ay7(A:B) 1rghB 15 75.0 100 27.3 17.6 53.8 33.3 0 0 1a19B 15 60.0 80.0 72.7 53.3 92.9 81.2 0 0
1cgi(E:I) 2cgaB 33 64.3 27.3 100 55.2 56.0 48.2 96.2 75.8 1hpt_ 19 93.3 73.7 100 36.8 89.5 77.3 100 63.2
1d6r(A:I) 2tgt_ 27 43.8 25.9 54.5 28.6 53.6 71.4 73.9 63.0 1k9bA 13 66.7 92.3 44.4 53.3 35.7 15.2 22.2 15.4
1dfj(E:I) 9rsaB 29 41.0 55.2 64.3 26.5 57.7 48.4 55.0 37.9 2bnh_ 33 43.5 60.6 81.3 31.0 32.4 91.7 21.3 30.3
1e6e(A:B) 1e1nA 20 42.3 55.0 0 0 26.9 43.8 14.9 55.0 1cjeD 23 65.2 65.2 93.3 50.0 79.2 73.1 15.4 17.4
1eaw(A:B) 1eaxA 22 21.1 18.2 100 48.0 46.8 60.0 66.7 72.7 9pti_ 14 52.6 71.4 100 42.9 95.0 79.2 8.3 7.1
1ewy(A:C) 1gjrA 19 57.1 84.2 9.1 5.3 5.6 8.3 16.7 52.6 1czpA 17 51.6 94.1 57.1 42.1 63.2 63.2 50.0 41.2
1f34(A:B) 4pep_ 25 44.8 52.0 30.8 12.5 30.3 52.6 47.5 76.0 1f32A 24 57.9 45.8 72.7 24.2 55.2 69.6 70.4 79.2
1mah(A:F) 1j06B 27 35.9 51.9 16.7 3.4 28.0 63.6 36.6 96.3 1fsc_ 21 86.4 90.5 15.8 15.0 33.3 21.9 33.3 28.6
1ppe(E:I) 1btp_ 27 64.9 88.9 64.3 42.9 40.9 42.8 0 0 1lu0A 14 63.2 85.7 92.3 75.0 100 56.0 90.0 64.3
1tmq(A:B) 1jae_ 28 62.2 82.1 75.0 40.0 36.0 30.0 63.4 92.9 1b1uA 26 57.1 76.9 93.3 56.0 70.4 76.0 0 0
1udi(E:I) 1udh_ 26 52.2 46.2 63.6 25.9 48.0 66.7 72.0 69.2 2ugiB 26 94.4 65.4 92.9 56.5 72.7 80.0 85.7 46.2
2pcc(A:B) 1ccp_ 13 20.0 23.1 53.8 50.0 26.7 33.3 0 0 1ycc_ 14 26.3 35.7 42.9 35.3 37.5 33.3 13.3 14.3
2sic(E:I) 1sup_ 26 50.0 46.2 72.7 38.1 81.8 60.0 62.5 76.9 3ssi_ 12 84.6 91.7 0 0 100 72.2 0 0
2sni(E:I) 1ubnA 27 66.7 59.3 60.0 33.3 60.0 83.0 66.7 81.5 2ci2I 15 42.9 40.0 57.1 57.1 0 0 76.9 66.7
7cei(A:B) 1unkD 20 76.9 50.0 75.0 35.3 47.4 60.0 75.0 45.0 1m08B 16 64.3 56.3 40.0 37.5 0 0 13.8 25.0
others  
1ak4(A:D) 2cpl_ 17 42.9 35.3 50.0 31.3 33.3 18.8 59.1 76.5 1e6jP 9 30.4 77.8 0 0 0 0 0 0
1atn(A:D) 1ijjB 17 5.3 5.9 0 0 20.7 37.5 0 0 3dni_ 24 40.0 33.3 0 0 0 0 66.7 66.7
1b6c(A:B) 1d6oA 20 54.3 95.0 83.3 55.6 40.0 11.1 93.3 70.0 1iasA 20 44.0 55.0 54.5 25.0 31.6 25.0 0 0
1buh(A:B) 1hcl_ 16 68.4 81.3 0 0 6.3 11.8 0 0 1dksA 18 75.0 83.3 58.3 38.9 36.4 22.2 100 66.7
1e96(A:B) 1mh1_ 14 66.7 85.7 38.5 25.0 46.2 60.0 10.0 14.3 1hh8A 12 73.3 91.7 41.7 35.7 45.5 35.7 0 0
1fq1(A:B) 1fpzF 16 63.2 75.0 0 0 0 0 0 0 1b39A 16 63.2 75.0 0 0 30.0 23.1 17.1 37.5
1fqj(A:B) 1tndC 21 20.7 81.0 70.6 42.9 32.3 35.7 28.6 38.1 1fqiA 24 18.9 58.3 90.9 47.6 42.9 14.3 78.9 62.5
1gcq(B:C) 1griB 14 35.3 42.9 70.0 63.6 38.9 63.6 22.2 14.3 1gcpB 18 78.9 83.3 60.0 40.0 100 33.3 33.3 16.7
1ghq(A:B) 1c3d_ 10 41.7 100 0 0 42.9 37.5 0 0 1ly2A 9 47.4 100 0 0 42.9 66.7 8.7 22.2
1grn(A:B) 1a4rA 17 54.2 76.5 33.3 15.0 40.0 40.0 50.0 58.8 1rgp_ 22 50.0 54.5 16.7 4.5 100 13.6 78.9 68.2
1h1v(A:G) 1ijjB 24 28.6 41.7 46.2 13.0 35.3 26.1 38.8 76.0 1d0nB 25 43.8 56.0 0 0 40.0 4.9 4.7 12.0
1he1(C:A) 1mh1_ 16 48.0 75.0 66.7 30.8 50.0 42.3 0 0 1he9A 21 40.9 42.9 76.5 46.4 33.3 7.1 0 0
1he8(B:A) 821P_ 13 20.6 100 0 0 43.8 33.3 26.7 61.5 1e8zA 15 11.1 53.3 42.9 16.7 5.9 5.6 0.6 6.7
1i2m(A:B) 1qg4A 24 14.3 33.3 42.9 21.4 43.8 50.0 15.0 12.5 1a12A 32 15.1 43.8 0 0 50.0 5.1 48.0 75.0
1ibr(A:B) 1qg4A 35 43.2 45.7 73.3 22.0 55.0 22.0 14.3 8.6 1f59A 42 38.9 33.3 7.1 1.8 0 0 10.3 16.7
1kac(A:B) 1nobF 15 68.4 86.7 0 0 15.4 21.1 0 0 1f5wB 21 83.3 95.2 60.0 28.6 71.4 23.8 35.3 28.6
1ktz(A:B) 1tgk_ 9 26.7 44.4 45.5 62.5 13.3 25.0 50.0 88.9 1m9zA 12 57.1 100 66.7 80.0 60.0 60.0 33.3 50.0
1kxp(A:D) 1ijjB 34 13.6 8.8 81.3 30.2 45.5 23.3 4.3 5.9 1kw2B 41 32.0 19.5 0 0 75.0 13.0 48.9 56.1
1kxq(H:A) 1kxqH 25 12.1 16.0 91.7 30.6 78.6 30.6 18.2 8.0 1ppi_ 30 22.7 16.7 41.7 17.9 20.0 3.6 47.8 73.3
1m10(A:B) 1auq_ 24 57.1 50.0 58.3 24.1 65.0 44.8 50.0 45.8 1mozB 29 68.0 58.6 0 0 31.6 18.2 0 0
1qa9(A:B) 1hnf_ 16 76.2 100 0 0 27.3 17.6 10.0 12.5 1cczA 16 82.4 87.5 6.7 5.3 22.2 10.5 28.6 25.0
1sbb(A:B) 1bec_ 13 54.2 100 0 0 17.6 17.6 0 0 1se4_ 11 50.0 100 0 0 50.0 12.5 10.0 27.3
1wq1(R:G) 6q21D 26 61.5 61.5 66.7 32.3 41.7 32.2 76.2 61.5 1wer_ 33 62.5 45.5 100 26.5 36.4 11.8 70.0 63.6
2btf(A:P) 1ijjB 26 63.3 73.1 53.3 32.0 25.0 12.0 22.0 42.3 1pne_ 23 56.0 60.9 0 0 70.0 28.0 0 0
  1. aPDB is the unbound structure of the two proteins in complex.
  2. bInt n is the number of residues on actual interface in complex.
  3. cAcc (%) is the accuracy of the corresponding method on the data set.
  4. dCov (%) is the coverage of the corresponding method on the data set.
  5. eE-I is the type of enzyme-inhibitor.
  6. fThe values for metaPPI and meta-PPISP are from literatures [14].
  7. gThe results for PPI-Pred are calculated by using the same definition of actual interface with DoBi.
  8. hThe binding sites between chain E and chain I of 1acb are predicted by each method; Two unbound structures are chain B of 2cga and the only one chain of 1egl.