Table 1.
Pathwalking results on simulated density maps. A summarized table of pathwalking on the benchmark of 40 5 Å simulated density maps. Reported resolution and number of amino acids for each protein is shown. Additionally, 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 the table were from the LKH-TSP solver, though nearly identical results were obtained with the Concorde TSP search method. Images of all 40 pathwalking models can be found in Figure S4.
| PDB ID |
Length (aa) |
RMSD (Å) |
Cα within 3Å radius (%) |
Cα within 5Å radius (%) |
Correctly registered Cαs (%) |
Topology score |
|---|---|---|---|---|---|---|
| Alpha | ||||||
| 1h12 | 404 | 5.66 | 20.8 | 46 | 12.1 | 0.84 |
| 1oai | 59 | 1.67 | 84.8 | 100 | 78 | 1.00 |
| 1ppr | 155 | 2.73 | 60.7 | 96.1 | 32.3 | 0.82 |
| 1qsa | 363 | 6.28 | 3.6 | 28.7 | 3 | 0.89 |
| 2erl | 40 | 1.70 | 85 | 100 | 77.5 | 1.00 |
| Alpha/Beta | ||||||
| 1b25 | 209 | 2.36 | 66.5 | 97.1 | 48.3 | 0.88 |
| 1ejd | 207 | 2.14 | 70.5 | 99.5 | 60.4 | 1.00 |
| 1ewf | 180 | 5.18 | 24.4 | 54.4 | 20.6 | 1.00 |
| 1h70 | 255 | 2.15 | 76.1 | 98.0 | 54.1 | 1.00 |
| 1igd | 61 | 2.42 | 57.4 | 100 | 50.8 | 1.00 |
| 1j0p | 108 | 3.96 | 29.6 | 69.4 | 13 | 1.00 |
| 1ogq | 313 | 3.88 | 39.6 | 70.9 | 14.1 | 0.82 |
| 1plq | 258 | 2.97 | 54.7 | 84.5 | 42.6 | 0.94 |
| 1vbw | 68 | 1.36 | 98.5 | 100 | 86.8 | 1.00 |
| 1vq8 | 115 | 5.37 | 34.8 | 48.7 | 27.8 | 1.00 |
| 1wru | 88 | 2.04 | 80.7 | 100 | 58 | 1.00 |
| 2eiy | 164 | 3.93 | 31.1 | 75 | 23.8 | 0.96 |
| 2hba | 52 | 3.69 | 44.2 | 84.6 | 7.7 | 1.00 |
| 3hms | 91 | 1.49 | 89.0 | 95.6 | 84.6 | 1.00 |
| Beta | ||||||
| 1a1x | 106 | 3.03 | 64.2 | 89.6 | 17 | 0.95 |
| 1auu | 55 | 2.62 | 65.5 | 87.3 | 56.4 | 1.00 |
| 1h8p | 44 | 1.92 | 88.6 | 100 | 50 | 1.00 |
| 1i5p | 198 | 3.04 | 56.1 | 83.8 | 43.9 | 0.93 |
| 1iwm | 177 | 5.68 | 23.2 | 45.8 | 11.3 | 1.00 |
| 1lkt | 104 | 3.03 | 39.4 | 98.1 | 26.9 | 1.00 |
| 1m3y | 188 | 5.99 | 13.3 | 38.3 | 7.4 | 0.96 |
| 1mkn | 59 | 1.50 | 86.4 | 100 | 78 | 1.00 |
| 1n7v | 177 | 6.54 | 17.5 | 40.1 | 10.7 | 1.00 |
| 1p9h | 159 | 4.59 | 37.1 | 56 | 22 | 0.91 |
| 1rg8 | 141 | 3.01 | 51.1 | 87.2 | 36.9 | 1.00 |
| 1tl2 | 235 | 2.20 | 77 | 99.6 | 44.7 | 0.90 |
| 1v3w | 173 | 4.12 | 32.4 | 56.1 | 26.6 | 1.00 |
| 1w6s | 595 | 5.76 | 21.3 | 47.2 | 11.4 | 0.95 |
| 1yfq | 342 | 4.53 | 30.1 | 66.4 | 17.8 | 0.95 |
| 2bf6 | 383 | 3.66 | 41.5 | 73.1 | 23 | 1.00 |
| 2bmo | 137 | 2.15 | 75.9 | 97.1 | 54 | 0.91 |
| 2dpf | 111 | 2.33 | 67.6 | 97.3 | 49.5 | 1.00 |
| 2hnu | 81 | 2.09 | 75.3 | 100 | 58 | 1.00 |
| 3c7x | 196 | 2.35 | 73 | 90.3 | 59.7 | 0.83 |
| Irregular | ||||||
| 1ba3 | 53 | 1.73 | 98.1 | 100 | 60.4 | 1.00 |