Skip to main content

Table 8 Detailed Comparison to PINUP and ProMate

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

PDBa Complex Int n b DoBi PINUPg ProMatef
    Accc Covd Acc Cov Acc Cov
1a19A 1brs(A:D) 16 86.7 81.3 72.2 81.3 100 29
1a2pA 1brs(D:A) 19 76.2 84.2 63.6 73.7 90 19
1a5e_ 1bi7(B:A) 30 82.1 76.7 41.2 23.3 88 10
1acl_ 1fss(A:B) 25 36.7 72.0 35.9 56.0 24 14
1ag6_ 2pcf(A:B) 24 65.0 54.2 56.3 37.5 70 16
1aje_ 1am4(D:A) 18 57.1 22.2 60.0 33.3 72 30
1ajw_ 1cc0(E:A) 9 50.0 88.9 66.7 66.7 73 24
1aueA 1fap(B:A) 8 58.3 87.5 15.8 37.5 90 35
1avu_ 1avw(B:A) 15 30.0 40.0 66.7 93.3 100 29
1aye_ 1dtd(A:B) 22 42.1 36.4 44.4 54.5 54 24
1b1eA 1a4y(B:A) 32 38.7 37.5 88.2 46.9 69 24
1bip_ 1tmq(B:A) 29 66.7 55.2 61.1 37.9 100 27
1ctm_ 2pcf(B:A) 21 62.1 85.7 38.1 38.1 100 12
1cto_ 1cd9(B:A) 6 40.0 33.3 35.3 100 36 29
1cye_ 1eay(A:B) 16 55.6 62.5 5.6 6.3 0 0
1d0nA 1c0f(S:A) 27 46.2 44.4 0 0 67 3
1d2bA 1uea(B:A) 19 66.7 52.6 78.6 57.9 92 31
1ekxA 1d09(A:B) 21 64.5 95.2 0 0 0 0
1ex3A 1cgi(E:I) 33 61.1 33.3 68.2 45.5 100 29
1ez3A 1dn1(B:A) 18 88.9 44.4 47.1 44.4 100 6
1eza_ 3eza(A:B) 21 64.0 76.2 0 0 0 0
1eztA 1agr(E:A) 22 57.1 54.5 22.2 18.2 54 13
1f00I 1f02(I:T) 17 31.6 35.3 0 0 0 0
1f5wA 1kac(B:A) 21 71.4 71.4 25.0 23.8 100 6
1fkl_ 1b6c(A:B) 19 54.5 63.2 75.0 47.4 100 20
1flzA 1eui(A:C) 25 42.9 96.0 77.3 68.0 52 19
1fvhA 1dn1(A:B) 42 51.4 45.2 53.3 38.1 0 0
1g4kA 1uea(A:B) 30 46.2 40.0 43.8 23.3 78 21
1gc7A 1ef1(A:C) 18 71.4 55.6 28.6 11.1 78 6
1gnc_ 1cd9(A:B) 15 43.7 46.7 21.4 20.0 6 2
1hh8A 1e96(B:A) 14 50.0 35.7 44.0 78.6 50 2
1hplA 1eth(A:B) 19 20.0 36.8 8.7 10.5 7 3
1hu8A 1ycs(A:B) 8 37.5 75.0 31.6 75.0 5 2
1iob_ 1itb(A:B) 38 38.1 21.1 46.7 18.4 31 6
1j6zA 1c0f(A:S) 29 28.2 75.9 34.6 31.0 0 0
1jae_ 1tmq(A:B) 32 60.0 65.6 83.3 46.9 50 13
1lba_ 1aro(L:P) 16 8.6 18.8 40.0 37.5 60 24
1nobA 1kac(A:B) 15 50.0 73.3 0 0 7 3
1nos_ 1noc(A:B) 9 33.3 44.4 0 0 0 0
1pco_ 1eth(B:A) 15 77.8 46.7 16.7 20.0 60 12
1pne_ 1hlu(P:A) 25 65.7 92.0 93.8 60.0 0 0
1poh_ 1ggr(B:A) 10 57.1 40.0 72.7 80.0 0 0
1ppp_ 1stf(E:I) 29 79.3 79.3 47.4 31.0 91 30
1qqrA 1bml(C:A) 7 33.3 28.6 38.5 71.4 85 32
1rgp_ 1am4(A:D) 16 55.0 68.8 36.8 43.8 50 5
1selA 1cse(E:I) 29 75.0 93.1 60.9 48.3 61 27
1vin_ 1fin(B:A) 29 40.0 34.5 50.0 51.7 0 0
1wer_ 1wq1(G:R) 33 67.7 63.6 70.6 36.4 0 0
1xpb_ 1jtg(A:B) 32 69.2 56.3 89.5 53.1 0 0
2bnh_ 1a4y(A:B) 38 38.5 39.5 37.8 36.8 100 4
2cpl_ 1ak4(A:D) 17 61.9 76.5 78.6 64.7 76 23
2f3gA 1ggr(A:B) 18 50.0 50.0 64.7 61.1 100 12
2nef_ 1avz(B:A) 10 56.3 90.0 30.8 40.0 57 24
2rgf_ 1lfd(A:B) 14 52.4 78.6 27.8 35.7 20 5
3ssi_ 2sic(I:E) 15 80.0 80.0 68.2 100 100 24
6ccp_ 2pcb(A:B) 9 23.5 44.4 28.6 66.7 0 0
Bounde 1jtg(B:A) 32 81.1 93.8 65.0 40.6 94 22
  1. aPDB is the unbound structure of the predicted protein.
  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. eThe unbound structure of 1jtgB was not available in PDB, and we used the bound structure instead.
  6. fThe values for ProMate are from literature [9].
  7. gThe results for PINUP are calculated by using the same definition of actual interface with DoBi.