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.
| 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 |