Table 1.
Transmembrane protein benchmark
| PDB | Name | Seq/len | Full protein | Converged | Aligned | |||
|---|---|---|---|---|---|---|---|---|
| rmsd | Length | rmsd | Length | rmsd | Length | |||
| 4HE8_H (3.3) | NADH-quinone oxidoreductase subunit 8 | 17.3 | 4.9 | 269 | 2.1 | 183 | 2.2 | 234 |
| 1SOR_A (N/A) | Aquaporin-0 | 26.2 | 2.7 | 221 | 2.1 | 188 | 2.0 | 200 |
| 4Q2E_A (3.4) | Phosphatidate cytidylyltransferase | 18.6 | 5.4 | 262 | 3.5 | 176 | 2.8 | 178 |
| 4HTT_A (6.8) | Sec-independent protein translocase protein | 14.6 | 3.9 | 225 | 1.8 | 124 | 2.4 | 181 |
| 4P6V_E (3.5) | Na(+)-translocating NADH-quinone reductase subunit D | 14.3 | 5.0 | 194 | 1.4 | 49 | 2.8 | 155 |
| 4J72_A (3.3) | Phospho-N-acetylmuramoyl-pentapeptide-transferase | 19.9 | 6.6 | 323 | 3.1 | 251 | 2.4 | 237 |
| 3V5U_A (1.9) | Sodium/Calcium exchanger | 10.2 | 3.9 | 297 | 3.7 | 284 | 2.3 | 245 |
| 4PGS_A (2.5) | Uncharacterized protein YetJ | 15.4 | 3.5 | 207 | 2.7 | 175 | 2.2 | 183 |
| 4QTN_A (2.8) | Vitamin B3 transporter PnuC | 9.0 | 4.2 | 202 | 3.0 | 155 | 2.8 | 178 |
| 4OD4_A (3.3) | 4-hydroxybenzoate octaprenyltransferase | 22.8 | 3.9 | 275 | 3.4 | 242 | 2.8 | 231 |
| 4O6M_A (1.9) | CDP-alcohol phosphotransferase | 13.3 | 4.1 | 188 | 4.0 | 165 | 2.3 | 159 |
| 4WD8_A (2.3) | Bestrophin domain protein | 5.94 | N/A | 268 | Not converged | |||
| 4F35_A (3.2) | Transporter, NadC family | 14.5 | N/A | 434 | Not converged | |||
Column 1, PDB code (resolution of the crystal structure); column 2, protein name; column 3, sequences per length, after filtering to reduce the redundancy to 90%; column 4, RMSD of predicted structure to native structure; column 5, length of native structure modeled; column 6, RMSD over converged and constrained region; column 7, length of converged and constrained region; column 8, RMSD over TM-align structural alignment; column 9, length of structurally aligned region.