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Table 7 Blind tests of dimer interface recognition: the rank of the native structure. aThe top (1AVZ-2SIC) and middle groups are the Sternberg and Vakser test sets, respectively (see Methods). The lower group (T04–T19) are the 2005 CAPRI target structures. bColumns 2–5 correspond to the energy functions optimized with OS1 and OS2, using 20, 4, or 6 amino acid classes, as indicated.cEnergy functions from Refs. [19], [20]. Numbers in bold show cases where the native structure is ranked among the top ten structures.

From: Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets

PDB IDa 20Cl OS1b 20Cl OS2 6Cl OS2 4Cl OS2 Luc Bastollac
1AVZ 73 35 67 100 54 40
1BGS 1 65 62 39 16 1
1BRC 76 37 41 31 5 70
1CGI 56 1 1 1 1 18
1DFJ 100 100 100 100 78 100
1FSS 24 1 1 1 1 1
1UGH 11 10 20 10 10 71
1WQ1 99 100 100 100 97 98
2PCC 20 72 82 79 25 23
2SIC 17 48 56 17 14 96
5CHA-2OVO 6 7 3 2 2 3
2PTN-4PTI 5 9 9 33 4 10
1SUP-2CI2 4 4 4 4 5 9
1A2P-1A19 31 58 52 27 20 17
1CHG-1HPT 2 7 4 6 2 4
T04 9 8 10 11 11 1
T05 64 61 62 62 60 60
T06 2 3 3 1 4 3
T07 58 63 62 56 58 64
T08 84 52 68 96 136 145
T09 165 162 164 165 159 164
T11 1 1 2 1 1 1
T12 9 5 6 2 1 5
T13 194 176 179 175 174 175
T14 68 121 91 125 18 43
T15 12 3 4 7 1 1
T18 25 8 7 1 2 4
T19 3 38 22 1 37 6