Table 4.
A comparison of protein tertiary structure prediction accuracy with ProtInfo web server and ROBETTA software available in the public domain for 50 test proteins
| Sl. No. | PDB ID | RMSD without end loops (Å) (Bhageerath) | RMSD without end loops (Å) (ProtInfo)a (30) | RMSD without end loops (Å) (ROBETTA)a (28) |
|---|---|---|---|---|
| 1 | 1E0Q | 4.5, 2.5, 3.0, 5.0, 3.4, 3.3, 3.2, 3.3, 5.9, 3.3 | 4.0, 4.1, 3.7, 3.9, 4.2 | 1.1b |
| 2 | 1B03 | 10.3, 4.4, 5.9, 5.5, 6.7, 5.4, 4.5, 6.1, 6.9, 7.5 | 4.0, 4.7, 4.1, 4.5, 4.4 | 2.7, 3.0 |
| 3 | 1WQC | 4.0, 4.5, 2.5, 3.8, 2.9, 5.1, 4.2, 5.7, 3.8, 4.7 | 2.1, 1.8, 1.8, 2.0, 2.1 | 2.3, 3.4 |
| 4 | 1RJU | 6.1, 6.3, 6.6, 5.9, 6.6, 5.9, 6.6, 7.0, 6.7, 7.4 | 3.4, 4.9, 3.3, 4.8, 6.0 | 3.4, 4.0, 2.5, 3.2, 3.0, 3.6, 4.8, 2.9, 3.0, 3.1 |
| 5 | 1EDM | 3.9, 3.5, 3.8, 4.0, 3.6, 5.2, 5.4, 4.1, 3.9, 4.7 | 3.4, 4.0, 3.7, 3.3, 3.1 | 0.4, 0.5, 0.4, 0.5, 0.6, 0.4, 0.7, 0.7, 1.1, 0.4 |
| 6 | 1AB1 | 4.8, 4.5, 4.3, 5.2, 4.2, 2.9, 4.5, 3.8, 5.8, 3.3 | 3.3, 5.1, 6.3, 3.6, 4.9 | 2.2, 2.8, 2.9, 2.4, 2.9, 2.7, 3.7, 3.5, 2.2, 3.3 |
| 7 | 1BX7 | 3.3, 4.0, 5.0, 3.2, 4.5, 3.8, 4.8, 3.1, 4.0, 3.5 | 2.6, 4.2, 3.7, 4.5, 2.1 | 0.9, 1.5, 1.0, 1.6, 1.5, 1.6, 1.4, 1.0, 2.0, 1.5 |
| 8 | 1B6Q | 6.1, 8.4, 4.0, 4.4, 3.8, 10.1, 5.3, 9.7, 10.7, 3.1 | 10.2, 10.0, 10.0, 10.4, 10.5 | 10.0, 9.6, 8.5, 7.6, 12.0, 8.3, 8.2, 7.0, 10.2, 9.0 |
| 9 | 1ROP | 5.3, 4.3, 9.2, 7.3, 7.5, 11.0, 14.2, 11.5, 8.7, 6.2 | 10.8, 11.5, 11.5, 10.1, 12.4 | 5.8, 10.3, 10.0, 11.7, 8.6, 7.0, 8.3, 7.7, 11.2, 13.6 |
| 10 | 1NKD | 3.9, 16.2, 10.1, 7.0, 10.6, 3.8, 4.8, 4.9, 7.9, 14.7 | 13.5, 13.5, 13.3, 13.4, 11.7 | 8.9, 8.9, 10.6, 11.0, 12.6, 10.7, 12.2, 10.1, 11.0, 9.1 |
| 11 | 1RPO | 9.9, 3.8, 4.0, 7.5, 14.4, 4.8, 6.0, 13.5, 3.8, 7.5 | 10.8, 10.4, 10.4, 10.9, 11.2 | 10.3, 8.7, 6.9, 6.0, 12.4, 7.7, 10.1, 7.2, 10.0, 7.7 |
| 12 | 1QR8 | 9.0, 11.1, 8.2, 7.1, 9.7, 14.0, 8.1, 10.9, 5.4, 4.4 | 10.1, 9.5, 10.0, 10.4, 12.2 | 11.3, 9.3, 9.0, 7.6, 9.5, 12.2, 10.5, 7.1, 11.3, 8.5 |
| 13 | 1FME | 4.9, 5.0, 4.8, 6.5, 3.7, 4.5, 4.2, 6.2, 4.3, 4.1 | 2.2, 2.3, 2.5, 2.7, 1.6 | 3.8, 2.8, 3.3, 4.5, 3.6, 3.1, 2.7, 3.9, 4.4, 3.7 |
| 14 | 1ACW | 5.5, 7.0, 5.3, 6.0, 7.4, 5.7, 7.0, 5.1, 7.2, 5.6 | 5.8, 5.8, 6.0, 6.2, 7.1 | 1.3, 1.7 |
| 15 | 1DFN | 5.0, 5.9, 6.5, 5.8, 6.8, 6.0, 7.1, 6.1, 6.5, 7.4 | 5.6, 6.8, 6.4, 6.6, 6.4 | 1.7, 5.3, 6.0, 5.5, 4.0, 6.3, 5.2, 6.5, 5.2, 6.6 |
| 16 | 1Q2K | 7.4, 7.4, 7.2, 4.8, 5.8, 6.5, 5.7, 6.2, 4.2, 7.3 | 5.9, 6.0, 5.8, 6.4, 9.1 | 1.7, 3.0, 3.3, 1.6, 4.7 |
| 17 | 1SCY | 6.1, 4.8, 6.6, 7.2, 3.1, 5.0, 6.5, 6.9, 7.2, 5.6 | 5.5, 5.6, 6.5, 6.4, 6.2 | 2.2, 2.7, 3.3 |
| 18 | 1XRX | 5.6, 8.8, 7.6, 7.7, 9.6, 8.4, 9.0, 6.2, 8.4, 8.2 | 8.6, 8.8, 7.8, 8.8, 4.0 | 5.2, 9.1, 7.1, 6.2, 4.4, 9.4, 6.6, 4.5, 5.4, 8.2 |
| 19 | 1ROO | 3.9, 3.4, 3.3, 3.8, 2.8, 4.1, 3.5, 3.2, 3.2, 3.3 | 2.8, 2.7, 2.7, 3.0, 2.7 | 1.8, 2.1, 1.9, 2.9, 2.5, 1.2, 2.5, 1.9, 2.8, 2.2 |
| 20 | 1YRF | 5.9, 5.7, 5.7, 4.8, 4.9, 5.0, 4.9, 5.0, 6.2, 5.8 | 4.3, 4.1, 3.3, 3.3, 4.3 | 1.7, 3.1, 4.3 |
| 21 | 1YRI | 5.9, 5.5, 4.6, 6.0, 5.5, 3.8, 5.5, 5.4, 5.5, 6.1 | 4.2, 4.0, 3.2, 3.2, 4.2 | 1.7, 3.9, 2.8 |
| 22 | 1VII | 5.5, 3.7, 6.6, 5.9, 6.1, 5.7, 5.6, 6.0, 6.3, 5.7 | 4.4, 4.7, 4.5, 4.3, 3.7 | 2.4, 3.3, 1.8, 5.6, 4.3, 3.0, 3.2, 3.7, 4.8, 1.9 |
| 23 | 1BGK | 5.8, 5.9, 4.1, 6.1, 5.8, 5.5, 5.5, 4.9, 5.2, 6.1 | 6.2, 6.0, 6.4, 6.4, 6.2 | 6.5, 4.1, 4.6, 2.5, 3.8, 5.9, 3.5, 3.3, 3.5, 6.1 |
| 24 | 1BHI | 7.9, 5.3, 6.7, 7.2, 5.4, 8.9, 6.3, 6.6, 6.2, 7.1 | 3.7, 3.8, 4.5, 4.5, 5.0 | 2.4, 2.4, 1.7, 1.1, 2.8, 1.7, 2.6, 2.2, 2.3, 1.9 |
| 25 | 1OVX | 4.0, 6.4, 6.3, 4.3, 6.1, 5.4, 5.3, 5.9, 7.7, 6.1 | 4.6, 4.9, 4.4, 5.6, 5.2 | 3.2, 1.5, 3.1, 2.6, 4.2, 4.4, 2.3, 2.6, 1.9, 5.0 |
| 26 | 1I6C | 7.5, 5.1, 5.4, 6.2, 5.4, 6.2, 8.0, 6.2, 6.7, 7.6 | 5.6, 5.7, 5.6, 7.3, 6.9 | 3.0, 3.0, 2.2, 3.2, 2.1 |
| 27 | 2ERL | 6.7, 8.6, 7.1, 8.4, 7.2, 3.2, 4.1, 6.2, 6.8, 8.1 | 7.0, 7.4, 7.1, 7.2, 8.3 | 1.3, 7.1 |
| 28 | 1RES | 6.1, 4.2, 5.2, 7.7, 4.8, 4.8, 4.3, 7.0, 5.6, 5.5 | 7.6, 7.1, 7.0, 7.3, 5.1 | 3.5, 3.0, 2.8, 4.3, 4.2, 2.3, 2.0 |
| 29 | 2CPG | 10.1, 5.3, 10.0, 8.5, 9.4, 10.6, 7.8, 9.4, 7.4, 7.5 | 4.2, 4.5, 5.3, 5.1, 11.0 | 8.0, 4.3, 8.5, 8.4, 6.5, 10.0, 4.8, 8.6, 5.5, 7.6 |
| 30 | 1DV0 | 7.7, 7.1, 8.0, 5.1, 8.3, 6.0, 7.8, 8.7, 8.4, 8.5 | 3.2, 4.4, 4.0, 2.8, 6.2 | 1.6, 1.5, 1.6, 2.0, 1.5, 4.5, 2.4, 2.0, 2.3, 4.2 |
| 31 | 1IRQ | 6.8, 6.9, 6.4, 6.7, 10.2, 8.4, 9.8, 9.0, 5.3, 8.2 | 8.2, 8.9, 9.1, 9.0, 8.5 | 6.1, 4.3, 6.0, 5.0, 6.6, 6.0, 7.4, 5.2, 6.4, 7.5 |
| 32 | 1GUU | 5.5, 5.3, 7.7, 4.6, 5.0, 4.6, 5.1, 5.7, 8.9, 9.1 | 10.1, 10.1, 9.8, 9.3, 10.1 | 2.9, 4.2, 2.9, 7.0, 3.2, 3.7, 2.4, 6.5, 5.6 |
| 33 | 1GV5 | 4.9, 4.1, 4.8, 4.8, 9.0, 9.4, 4.6, 9.2, 9.3, 8.9 | 9.4, 9.1, 9.5, 8.9, 3.3 | 8.5, 3.7, 9.1, 4.5, 4.7, 5.3, 4.2, 9.1, 3.1, 3.5 |
| 34 | 1GVD | 5.7, 6.4, 8.0, 5.1, 6.0, 4.9, 4.9, 6.9, 4.9, 5.5 | 9.4, 9.4, 8.8, 9.1, 3.9 | 8.5, 3.5, 2.7, 3.0, 4.7, 4.4, 4.3, 2.3, 6.7, 8.9 |
| 35 | 1MBH | 9.1, 9.2, 9.2, 4.0, 9.5, 8.4, 5.5, 5.5, 5.0, 5.3 | 4.3, 4.1, 5.7, 3.5, 9.5 | 8.3, 8.1, 4.2, 2.8, 8.9, 2.4, 7.9, 3.5, 7.7, 7.7 |
| 36 | 1GAB | 4.9, 9.2, 6.2, 6.0, 6.8, 3.6, 8.5, 9.7, 8.8, 6.3 | 5.5, 5.6, 6.4, 5.4, 5.9 | 2.3, 8.8, 2.7, 7.9, 2.8, 8.1, 2.7, 2.3, 2.2, 7.7 |
| 37 | 1MOF | 5.7, 3.7, 3.9, 4.2, 2.9, 4.0, 4.9, 4.3, 4.0, 4.9 | 12.7, 13.6, 12.5, 12.7, 13.5 | 13.7, 11.8, 11.2, 12.6, 12.6, 12.0, 12.2, 12.9, 12.8, 11.2 |
| 38 | 1ENH | 6.3, 9.9, 4.6, 9.1, 9.7, 5.8, 5.7, 9.5, 6.2, 6.4 | 5.0, 4.6, 4.3, 8.7, 4.2 | 2.2, 1.7, 1.8, 5.1, 2.3, 4.6, 3.0, 5.2, 3.1, 3.2 |
| 39 | 1IDY | 4.6, 4.9, 8.7, 4.0, 3.6, 3.5, 5.3, 3.7, 6.0, 9.3 | 8.7, 8.3, 8.3, 8.8, 4.6 | 2.7, 2.5, 3.0, 8.5, 2.1, 2.0, 2.1, 6.8, 2.6, 2.9 |
| 40 | 1PRV | 6.9, 5.1, 6.9, 5.8, 5.0, 5.6, 5.6, 9.5, 4.9, 4.9 | 2.3, 2.6, 3.0, 3.2, 5.4 | 2.5, 2.1, 3.4, 2.9, 3.7, 4.9, 2.9, 2.4, 4.2, 6.8 |
| 41 | 1HDD | 10.2, 6.3, 10.2, 5.5, 11.1, 6.2, 9.8, 4.8, 7.0, 6.7 | 4.4, 4.7, 5.8, 4.6, 9.7 | 2.3, 2.5, 2.2, 3.3, 3.6, 4.4, 3.4, 3.0, 4.2, 4.2 |
| 42 | 1BDC | 7.7, 6.1, 6.6, 8.3, 4.8, 7.0, 7.5, 5.0, 6.7, 6.6 | 3.1, 3.0, 3.5, 2.8, 5.1 | 2.5, 2.5, 3.7, 3.2, 7.7, 4.0, 3.7, 7.9, 2.6, 7.8 |
| 43 | 1I5X | 5.5, 5.9, 3.6, 5.4, 5.8, 2.6, 4.3, 6.0, 3.9, 5.1 | 11.4, 11.0, 11.0, 11.5, 9.2 | 10.8, 6.8, 8.6, 12.5, 4.5, 9.8, 7.1, 13.1, 9.0, 7.0 |
| 44 | 1I5Y | 5.8, 5.1, 4.3, 4.3, 3.4, 4.9, 2.6, 3.7, 3.2, 4.0 | 9.8, 8.9, 8.4, 11.8, 9.1 | 9.6, 7.8, 10.2, 9.1, 8.2, 5.0, 12.5, 11.3, 8.4, 8.1 |
| 45 | 1KU3 | 6.6, 7.4, 6.4, 5.5, 7.2, 5.6, 6.3, 6.2, 5.6, 8.3 | 5.6, 5.4, 4.9, 5.4, 9.6 | 4.7, 4.4, 5.8, 4.5, 5.3, 5.3, 5.5, 6.2, 4.7, 2.9 |
| 46 | 1YIB | 6.7, 5.3, 5.5, 5.8, 3.5, 4.8, 5.1, 4.5, 5.2, 4.6 | 17.5, 17.6, 18.3, 17.3, 17.4 | 17.8, 17.5, 17.1, 17.1, 17.3, 17.5, 18.5, 16.3 |
| 47 | 1DF5 | 3.4, 5.3, 6.0, 6.1, 7.0, 3.8, 3.4, 3.1, 8.1, 3.4 | 9.3, 10.3, 8.7, 9.3, 11.7 | 9.9, 8.2, 5.7, 5.6, 9.9, 8.5, 8.6, 11.1, 6.3, 7.0 |
| 48 | 1AHO | 7.8, 7.6, 9.1, 8.7, 6.6, 6.0, 7.2, 7.7, 9.2, 7.7 | 8.1, 6.6, 4.1, 5.2, 6.0 | 0.6, 1.1, 0.6, 1.2, 1.0, 0.4, 0.8, 1.4, 1.2, 0.8 |
| 49 | 1QR9 | 4.3, 3.8, 4.9, 5.1, 10.9, 6.0, 4.0, 4.0, 4.2, 4.6 | 11.0, 11.1, 9.6, 11.2, 12.9 | 6.3, 8.5, 4.3, 9.9, 8.6, 6.5, 8.7, 11.7, 12.1, 10.7 |
| 50 | 1AIL | 10.8, 6.6, 4.4, 6.4, 7.2, 8.9, 4.2, 8.5, 6.0, 4.2 | 9.0, 8.9, 8.4, 7.6, 10.3 | 3.2, 4.4, 4.5, 5.3, 7.2, 5.4, 6.4 |
aThe secondary structure information was utilized from the native structure along with the sequence information for both Bhageerath and ROBETTA (Rosetta++ software suite was obtained from UW TechTransfer Digital Ventures). We have generated 10000 decoys starting from sequence and secondary structure information. The top 2000 scoring decoys were selected and top 10 cluster centers were extracted. The ProtInfo (http://protinfo.compbio.washington.edu) predictions were obtained from the sequence information alone.
bFor the system 1e0q it took ∼12 days on a dedicated processor to generate 1000 decoys.