Table 3.
Pathwalking results on authentic density maps. A summarized table of all pathwalking generated models is presented. As in Table 1, the number of amino acids for each protein, resolution, the Cα RMS deviation, the percent of total Cαs within a 3 and 5 Å radius when compared to the corresponding Cα position in the known structure, the percent of correctly registered Cαs and the topology score from the CLICK webserver (0–1 where 1 corresponds to an identical topology between the known and pathwalker structures) are reported. The results summarized in this table were from the LKH-TSP solver. For RDV P8 and MM-cpn, only the results for the first pathwalker model are reported.
| Data set | Reported Resolution (Å) |
Number of Amino Acids |
Cα RMSD (Å) |
Cα within 3Å radius (%) |
Cα within 5Å radius (%) |
Correctly registered Cαs (%) |
Topology score |
|---|---|---|---|---|---|---|---|
| Aquaporin-1 | 3.8 | 220 | 4.63 | 27.3 | 57.7 | 25.5 | 1.00 |
| Rotavirus VP6 | 3.8 | 397 | 3.99 | 49.6 | 72.5 | 40.8 | 0.93 |
| GroEL | 4.0 | 524 | 7.51 | 12 | 35.8 | 10.3 | 0.79 |
| GroEL-Rosetta | 4.0 | 524 | 6.31 | 25.8 | 45.5 | 25.4 | 0.98 |
| Ribosome chain P | 6.4 | 84 | 3.08 | 4.51.8 | 83.1 | 45.8 | 0.88 |
| Ribosome chain Q | 6.4 | 100 | 4.42 | 36.4 | 69.7 | 31.3 | 1.00 |
| Ribosome chain H | 6.4 | 139 | 8.09 | 18.8 | 35.5 | 15.2 | 0.93 |
| Ribosome chain B | 6.4 | 220 | 9.86 | 3.2 | 15.4 | 4.1 | 0.96 |
| Ribosome chain G | 6.4 | 156 | 8.75 | 20 | 27.1 | 19.4 | 1.00 |
| Ribosome chain N | 6.4 | 61 | 4.89 | 21.7 | 47.7 | 15 | 1.00 |
| RDV P8* | 7.9 | 421 | 15.49 | 3.1 | 12.4 | 1 | 0.27 |
| MM-cpn* | 4.3 | 508 | 3.13 | 56.2 | 84.3 | 51.9 | 1.00 |
| Epsilon 15 gp7 | 4.5 | 335 | 9.02 | 4.2 | 14 | 5.1 | 0.75 |