Table 2.
Leave-one-out cross validation for 57 unbound protein structures
| Unbound proteina | PDB code | Complex code | interface residues | Surface residues | Coverage (%) | Accuracy (%) |
|---|---|---|---|---|---|---|
| Barstar | 1a19A | 1brsA | 17 | 70 | 82.4 | 73.7 |
| Barnase | 1a2pA | 1brsD | 18 | 91 | 72.2 | 61.9 |
| Tumor suppressor p16ink4a | 1a5e- | 1bi7B | 31 | 125 | 22.6 | 38.9 |
| Acetylcholinesterase | 1acl- | 1fssA | 25 | 355 | 56.0 | 35.9 |
| Plastocyanin | 1ag6- | 2pcfA | 23 | 78 | 39.1 | 60.0 |
| cdc42hs | 1aje- | 1am4D | 18 | 160 | 33.3 | 60.0 |
| Rhogdi | 1ajw- | 1cc0E | 13 | 127 | 69.2 | 69.2 |
| Fkbp-rapamycin-binding domain | 1aueA | 1fapB | 8 | 78 | 37.5 | 15.8 |
| Trypsin inhibitor | 1avu- | 1avwB | 15 | 138 | 93.3 | 66.7 |
| Human procarboxypeptidase a2 | 1aye- | 1dtdA | 24 | 304 | 54.2 | 44.8 |
| Hydrolase angiogenin | 1b1eA | 1a4yB | 34 | 101 | 47.1 | 88.9 |
| Bifunctional trypsin/alpha-amylase inhibitor (rbi) | 1bip- | 1tmqB | 27 | 119 | 37.0 | 58.8 |
| Cytochrome f | 1ctm- | 2pcfB | 25 | 201 | 36.0 | 36.0 |
| Granulocyte colony stimulating factor | 1cto- | 1cd9B | 6 | 103 | 100.0 | 35.3 |
| Receptor chey mutant | 1cye- | 1eayA | 13 | 97 | 7.7 | 6.7 |
| Calcium-free equine plasma gelsolin | 1d0nA | 1c0fS | 24 | 589 | 0.0 | 0.0 |
| Hydrolase inhibitor | 1d2bA | 1ueaB | 22 | 109 | 59.1 | 81.2 |
| Transferase | 1ekxA | 1d09A | 21 | 232 | 0.0 | 0.0 |
| Bovine chymotrypsinogen a | 1ex3A | 1cgiE | 28 | 188 | 46.4 | 68.4 |
| Neuronal t-snare syntaxin-1a | 1ez3A | 1dn1B | 18 | 116 | 44.4 | 47.1 |
| N-terminal domain of enzyme I from E.coli | 1eza- | 3ezaA | 24 | 249 | 0.0 | 0.0 |
| rgs4 | 1eztA | 1agrE | 21 | 115 | 19.0 | 23.5 |
| Enteropathogenic E.coli intimin C-terminal domain | 1f00I | 1f02I | 16 | 215 | 0.0 | 0.0 |
| Coxsackie virus and adenovirus receptor | 1f5wA | 1kacB | 18 | 98 | 22.2 | 23.5 |
| Fk506 binding protein | 1fkl- | 1b6cA | 20 | 88 | 45.0 | 69.2 |
| Uracil-DNA glycosylase | 1flzA | 1euiA | 26 | 172 | 69.2 | 78.3 |
| Neuronal sec1 | 1fvhA | 1dn1 | 41 | 423 | 39.0 | 55.2 |
| Hydrolase | 1g4kA | 1ueaA | 31 | 133 | 22.6 | 41.2 |
| Radixin ferm domain | 1gc7A | 1ef1A | 59 | 248 | 11.9 | 31.8 |
| Granulocyte colony stimulating factor (rhg-csf) | 1gnc- | 1cd9A | 18 | 174 | 16.7 | 17.6 |
| N-terminal region of p67phox | 1hh8A | 1e96B | 14 | 150 | 78.6 | 44.0 |
| Lipase (EC 3.1.1.3) | 1hplA | 1ethA | 21 | 325 | 9.5 | 8.0 |
| p53 core DNA-binding domain | 1hu8A | 1ycsA | 16 | 155 | 68.8 | 29.7 |
| Interleukin-1 beta | 1iob- | 1itbA | 42 | 133 | 19.0 | 47.1 |
| Actin | 1j6zA | 1c0fA | 30 | 281 | 30.0 | 33.3 |
| α-Amylase | 1jae- | 1tmqA | 33 | 316 | 45.5 | 78.9 |
| (EC 3.5.1.28) mutant | 1lba- | 1aroL | 16 | 112 | 37.5 | 40.0 |
| Knob domain from adenovirus serotype 12 | 1nobA | 1kacA | 18 | 139 | 0.0 | 0.0 |
| Nitric oxide synthase oxygenase domain | 1nos- | 1nocA | 1 | 251 | 0.0 | 0.0 |
| Porcine pancreatic procolipase b | 1pco- | 1ethB | 18 | 85 | 22.2 | 18.2 |
| Profilin | 1pne- | 1hluP | 25 | 107 | 60.0 | 93.8 |
| Phosphotransferase (hpr) | 1poh- | 1ggrB | 16 | 69 | 75.0 | 66.7 |
| Papain (EC 4.3.22.2) | 1ppp- | 1stfE | 28 | 160 | 32.1 | 50.0 |
| Streptokinase domain b | 1qqrA | 1bmlC | 10 | 118 | 70.0 | 38.9 |
| Rhogap | 1rgp- | 1am4A | 17 | 155 | 41.2 | 35.0 |
| Selenosubtilisin | 1selA | 1cseE | 23 | 177 | 47.8 | 61.1 |
| Cyclin a | 1vin- | 1finB | 29 | 194 | 51.7 | 50.0 |
| P120gap | 1wer- | 1wq1G | 34 | 251 | 35.3 | 66.7 |
| α-Lactamase tem1 | 1×pb- | 1jtgA | 33 | 186 | 54.5 | 90.0 |
| Ribonuclease inhibitor | 2bnh- | 1a4yA | 39 | 370 | 35.9 | 36.8 |
| Cyclophilin a | 2cpl- | 1ak4A | 19 | 120 | 63.2 | 75.0 |
| Glucose-specific phosphocarrier | 2f3gA | 1ggrA | 20 | 104 | 60.0 | 63.2 |
| Negative factor (fprotein) | 2nef- | 1avzB | 14 | 128 | 42.9 | 33.3 |
| RalGEF-rbd streptomyces | 2rgf- | 1lfdA | 15 | 79 | 33.3 | 26.3 |
| Subtilisin inhibitor | 3ssi- | 2sicI | 13 | 92 | 100.0 | 68.4 |
| Cytochrome c peroxidase (EC 1.11.1.5) mutant | 6ccp- | 2pcbA | 13 | 226 | 69.2 | 29.0 |
| BLIP | Bound | 1jtgB | 30 | 136 | 40.0 | 63.2 |
| Mean | 22 | 174 | 42.2 | 44.5 | ||
| Enzyme (25) | 21 | 174 | 43 | 47.3 | ||
| Inhibitor (7) | 21 | 149 | 68.6 | 65.6 | ||
| Others (25) | 23 | 181 | 34.1 | 35.8 |
aThe same dataset has been used by Neuvirth et al. (10) except BLIP. The unbound structure of BLIP was not available in PDB and we used the bound structure instead.