Table 2.
Details and prediction result of Cheng dataset (test set, 55 proteins) (values in parentheses are RMSD (Å))
| PDB IDa | Domain 1 | Domain 2 | Linker length | Linker region | Best rank of acceptable docking pose by PINE |
|---|---|---|---|---|---|
| 1A8PA | 2–92 | 109–258 | 16 | 93–108 | 1 (1.1) |
| 1AH5A | 3–216 | 226–313 | 9 | 217–225 | 1 (1.5) |
| 1AMMA† | 1–80 | 90–174 | 9 | 81–89 | 3 (0.9) |
| 1AORB | 1–204 | 218–605 | 13 | 205–217 | 1 (1.1) |
| 1AQHA | 1–348 | 362–448 | 13 | 349–361 | 1 (1.1) |
| 1AR4A | 1–80 | 94–201 | 13 | 81–93 | 1 (1.1) |
| 1AW7A | 1–89 | 98–194 | 8 | 90–97 | 1 (1.4) |
| 1AW9A | 2–76 | 95–217 | 18 | 77–94 | 1 (2.0) |
| 1B06A | 3–89 | 103–210 | 13 | 90–102 | 1 (1.7) |
| 1B25A | 1–202 | 216–619 | 13 | 203–215 | 1 (1.6) |
| 1B8PA | 3–156 | 161–329 | 4 | 157–160 | 1 (1.3) |
| 1BAGA† | 1–341 | 361–425 | 19 | 342–360 | 1 (1.1) |
| 1BAYA | 1–73 | 85–209 | 11 | 74–84 | 1 (0.8) |
| 1BIKA | 25–76 | 95–134 | 18 | 77–94 | 1 (1.2) |
| 1CA1A† | 1–245 | 259–370 | 13 | 246–258 | 2 (1.2) |
| 1CHMB | 2–155 | 166–402 | 10 | 156–165 | 5 (1.8) |
| 1CLCA† | 35–128 | 140–575 | 11 | 129–139 | 1 (1.7) |
| 1CLVA | 1–373 | 386–471 | 12 | 374–385 | 1 (1.4) |
| 1CR5B | 23–101 | 121–207 | 19 | 102–120 | 1 (0.9) |
| 1DLUB | 4–260 | 274–392 | 13 | 261–273 | 1 (1.5) |
| 1E5MA | 6–249 | 260–416 | 10 | 250–259 | 1 (1.1) |
| 1E9IB | 1–132 | 147–430 | 14 | 133–146 | 1 (1.4) |
| 1EBGA | 1–132 | 143–436 | 11 | 133–143 | 1 (1.4) |
| 1EE0A | 20–230 | 244–395 | 13 | 231–243 | 1 (1.6) |
| 1ET6B | 4–93 | 105–209 | 11 | 94–104 | 1 (1.7) |
| 1ET9A | 1–92 | 101–204 | 8 | 93–100 | 1 (1.5) |
| 1ETPB | 1–86 | 102–190 | 15 | 87–101 | 224 (1.1) |
| 1F2EA | 1–74 | 90–201 | 15 | 75–89 | 1 (1.0) |
| 1FDRA | 2–91 | 108–248 | 16 | 92–107 | 1 (1.6) |
| 1FFHA | 2–85 | 99–295 | 13 | 86–98 | 1 (0.8) |
| 1FFUF | 1–173 | 181–287 | 7 | 174–180 | 1 (0.9) |
| 1FIQB | 224–410 | 419–528 | 8 | 411–418 | 1 (1.7) |
| 1GK8C | 7–145 | 155–475 | 9 | 146–154 | 1 (1.7) |
| 1GSQA | 1–71 | 83–202 | 11 | 72–82 | 1 (1.6) |
| 1H1OB | 213–285 | 302–383 | 16 | 286–301 | 2 (0.9) |
| 1I8DB† | 1–86 | 105–206 | 18 | 87–104 | 2189 (0.9) |
| 1IK6A | 1–180 | 201–326 | 20 | 181–200 | 16 (1.0) |
| 1J3NA | 1–240 | 254–408 | 13 | 241–253 | 1 (1.0) |
| 1JLVA | 1–73 | 89–207 | 15 | 74–88 | 1 (1.0) |
| 1KGZA | 12–75 | 87–344 | 11 | 76–86 | 1 (1.2) |
| 1KZLA | 1–86 | 105–202 | 18 | 87–104 | 213 (1.1) |
| 1MB8A | 56–171 | 188–293 | 16 | 172–187 | 1 (3.9) |
| 1N5WF | 1–173 | 183–286 | 9 | 174–182 | 1 (1.7) |
| 1OE7A | 4–79 | 98–207 | 18 | 80–97 | 1 (0.8) |
| 1OI7A | 1–113 | 139–288 | 25 | 114–138 | 1 (9.5) |
| 1P5UA | 9–143 | 155–234 | 11 | 144–154 | 211 (2.1) |
| 1PBJA | 2–56 | 74–121 | 17 | 57–73 | 1 (1.1) |
| 1PDYA | 1–132 | 143–433 | 10 | 133–142 | 1 (1.3) |
| 1PGSA† | 4–145 | 150–314 | 14 | 136–149 | 1 (1.3) |
| 1PMTA | 1–74 | 8–8201 | 14 | 75–88 | 1 (1.7) |
| 1QNNA | 1–79 | 91–191 | 11 | 80–90 | 1 (1.4) |
| 1R5AA | 2–75 | 91–215 | 15 | 76–90 | 1 (1.7) |
| 1R6LA | 1–143 | 160–239 | 16 | 144–159 | 1 (1.4) |
| 1RWZA | 1–109 | 129–244 | 19 | 110–128 | 1 (1.1) |
| 1V8GA | 1–61 | 73–329 | 11 | 62–72 | 1 (1.4) |
a The first 4-letters are PDB ID and the 5th letter is chain ID. † It is also included in Wollacott dataset (Table 1).