Table 1.
Detail and prediction result of Wollacott dataset (training set, 62 proteins). (values in parentheses are RMSD (Å))
| PDB IDa | Domain 1 | Domain 2 | Linker length | Linker region | Best rank of acceptable docking pose | |
|---|---|---|---|---|---|---|
| Initial weight | Optimized weight | |||||
| 1A62A | 1–44 | 49–125 | 4 | 45–48 | 4 (1.2) | 2 (1.2) |
| 1A6QA | 2–290 | 299–368 | 8 | 291–298 | 1 (0.8) | 1 (0.8) |
| 1A79C | 9–81 | 85–179 | 3 | 82–84 | 1 (1.1) | 1 (1.1) |
| 1A8DA | 1–243 | 266–452 | 22 | 244–265 | 1 (1.6) | 1 (1.6) |
| 1A8LA | 1–116 | 123–226 | 6 | 117–122 | 1 (0.8) | 1 (1.4) |
| 1AMMA† | 1–80 | 90–174 | 9 | 81–89 | 6 (0.9) | 3 (0.9) |
| 1AOAA | 12–244 | 261–375 | 16 | 245–260 | 2 (1.8) | 1 (1.8) |
| 1AVAA | 1–343 | 352–403 | 8 | 344–351 | 1 (1.6) | 1 (1.6) |
| 1B63A | 2–215 | 218–331 | 2 | 216–217 | 1 (1.2) | 1 (1.3) |
| 1BAGA† | 1–343 | 361–425 | 19 | 342–360 | 1 (1.3) | 1 (1.1) |
| 1BG6A | 4–185 | 189–359 | 3 | 186–188 | 1 (1.7) | 1 (1.3) |
| 1BI5A | 1–232 | 237–389 | 4 | 233–236 | 1 (1.4) | 1 (1.4) |
| 1BKBA | 4–73 | 77–139 | 3 | 74–76 | 52 (7.7) | 10 (4.1) |
| 1BU6O | 3–252 | 260–499 | 7 | 253–259 | 1 (1.6) | 1 (1.6) |
| 1C2AA | 4–56 | 72–123 | 15 | 57–71 | 8965 (8.6) | 7455 (8.6) |
| 1CA1A† | 1–245 | 259–370 | 13 | 246–258 | 3 (1.2) | 2 (1.2) |
| 1CDYA | 1–96 | 99–178 | 2 | 97–98 | 4 (1.8) | 5 (1.8) |
| 1CJXB | 4–143 | 156–356 | 12 | 144–155 | 1 (1.6) | 1 (1.6) |
| 1CLCA† | 35–130 | 132–575 | 11 | 129–131 | 1 (1.8) | 1 (1.7) |
| 1CLIB | 1021–1168 | 1180–1345 | 11 | 1169–1179 | 1 (1.5) | 1 (1.5) |
| 1CRZA | 7–136 | 145–409 | 8 | 137–144 | 1183 (9.9) | 806 (9.9) |
| 1CTUA | 1–148 | 157–294 | 8 | 149–156 | 1 (2.4) | 1 (1.7) |
| 1CVRA | 1–339 | 356–432 | 16 | 340–355 | 1 (5.9) | 1 (5.9) |
| 1CX4A | 130–264 | 267–412 | 2 | 265–266 | 1 (1.8) | 1 (1.8) |
| 1D09B | 1–95 | 102–153 | 6 | 96–101 | 56 (4.3) | 173 (4.3) |
| 1D5RA | 14–184 | 192–351 | 7 | 185–191 | 1 (4.3) | 1 (4.3) |
| 1DZFA | 5–140 | 152–215 | 11 | 141–151 | 717 (7.9) | 520 (7.8) |
| 1EGAB | 4–171 | 190–296 | 18 | 172–189 | 78 (1.9) | 21 (1.9) |
| 1EOVA | 71–198 | 208–557 | 9 | 199–207 | 281 (9.7) | 440 (9.7) |
| 1EUDA | 1–128 | 134–306 | 5 | 129–133 | 1 (1.6) | 1 (1.4) |
| 1F1ZA | 8–167 | 170–267 | 2 | 168–169 | 1 (1.6) | 1 (1.6) |
| 1F3AA | 1–77 | 85–221 | 7 | 78–84 | 1 (1.4) | 1 (1.4) |
| 1F5NA | 7–276 | 290–583 | 13 | 277–289 | 1 (1.3) | 1 (1.3) |
| 1FMTA | 1–200 | 209–314 | 8 | 201–208 | 1441 (8.4) | 422 (1.1) |
| 1FTSA | 201–280 | 294–495 | 13 | 281–293 | 1 (1.1) | 1 (1.1) |
| 1GCYA | 1–355 | 362–418 | 6 | 356–361 | 1 (1.6) | 1 (1.6) |
| 1GV1B | 1–141 | 144–299 | 2 | 142–143 | 1 (1.3) | 1 (1.3) |
| 1HANA | 2–118 | 140–289 | 21 | 119–139 | 1 (1.4) | 1 (1.4) |
| 1HYEA | 1–144 | 149–313 | 4 | 145–148 | 1 (1.7) | 1 (1.7) |
| 1I8DB† | 1–86 | 105–206 | 18 | 87–104 | 891 (0.9) | 2189 (0.9) |
| 1J8MF | 3–83 | 99–297 | 15 | 84–98 | 1 (1.4) | 1 (1.4) |
| 1JAKA | 8–147 | 153–506 | 5 | 148–152 | 1 (1.7) | 1 (1.7) |
| 1JGTB | 2–206 | 219–508 | 12 | 207–218 | 1 (1.3) | 1 (1.3) |
| 1JPMA | 1–122 | 129–359 | 6 | 123–128 | 1 (1.3) | 1 (2.1) |
| 1JPNA | 1–85 | 99–296 | 13 | 86–98 | 1 (1.4) | 1 (1.4) |
| 1K0MA | 6–87 | 101–240 | 13 | 88–100 | 1 (1.4) | 1 (1.3) |
| 1KBWC | 13–155 | 165–314 | 9 | 156–164 | 1 (1.6) | 1 (1.6) |
| 1KNYA | 1–124 | 128–253 | 3 | 125–127 | 3 (1.8) | 8 (1.8) |
| 1KS9A | 1–165 | 169–291 | 3 | 166–168 | 1 (1.0) | 1 (1.3) |
| 1LAMA | 1–158 | 161–484 | 2 | 159–160 | 1 (1.2) | 1 (1.2) |
| 1LBUA | 1–76 | 88–213 | 11 | 77–87 | 1 (1.5) | 1 (1.5) |
| 1MGTA | 1–83 | 91–169 | 7 | 84–90 | 1 (1.5) | 1 (1.5) |
| 1NKRA | 6–99 | 109–200 | 9 | 100–108 | 398 (7.7) | 388 (9.0) |
| 1PGSA† | 4–135 | 150–314 | 14 | 136–149 | 1 (1.3) | 1 (1.3) |
| 1PIIA | 1–253 | 258–452 | 4 | 254–257 | 1 (1.9) | 1 (1.9) |
| 1QCSA | 0–83 | 87–201 | 3 | 84–86 | 3 (2.5) | 1 (8.1) |
| 1QFJC | 1–92 | 105–232 | 12 | 93–104 | 1 (1.0) | 1 (1.0) |
| 1QH4B | 2–99 | 112–381 | 12 | 100–111 | 1 (1.2) | 1 (1.2) |
| 1RHSA | 1–135 | 158–293 | 22 | 136–157 | 1 (1.4) | 1 (1.2) |
| 1SMDA | 1–401 | 406–496 | 4 | 402–405 | 1 (1.1) | 1 (1.1) |
| 1TF4B | 1–444 | 463–605 | 18 | 445–462 | 1880 (1.7) | 60 (2.6) |
| 2REBA | 3–266 | 270–328 | 3 | 267–269 | 1 (1.3) | 1 (1.3) |
a The first 4-letters are PDB ID and the 5th letter is chain ID. † It is also included in Cheng dataset (Table 2).