Table 1. Performance of conversion to all-atom structures from CG models with cg2all.
See also Figures S3 and S4.
| CG representation | Maximum number of beads per residue | RMSD1 | χ-angle accuracy1,2 | MolProbity1 | |||||
|---|---|---|---|---|---|---|---|---|---|
|
| |||||||||
| Backbone [Å] | Heavy atom [Å] | χ1 [%] | χ1+2 [%] | Score | Clash score | Rama favor [%] | Rotamer outlier [%] | ||
|
| |||||||||
| Experimental structure | - | - | - | - | - | 1.25 (0.34) | 3.2 (2.4) | 97.9 (1.2) | 1.4 (1.2) |
|
| |||||||||
| Rigid body reconstruction3 | - | 0.03 (0.01) | 0.16 (0.03) | - | - | 1.81 (0.29) | 12.2 (4.8) | 97.4 (1.3) | 1.4 (1.2) |
|
| |||||||||
| Cα | 1 | 0.18 (0.05) | 0.96 (0.12) | 86.2 (3.0) | 71.4 (4.8) | 2.07 (0.21) | 31.2 (9.5) | 97.9 (1.1) | 0.8 (0.7) |
| Cα (fixed)4 | 1 | 0.17 (0.05) | 0.93 (0.12) | 86.5 (3.0) | 71.8 (4.7) | 2.13 (0.21) | 34.2 (10.3) | 98.0 (1.1) | 1.0 (0.7) |
| N, Cα, C | 3 | 0.07 (0.02) | 0.83 (0.11) | 89.3 (2.8) | 75.7 (4.5) | 2.09 (0.23) | 27.6 (8.5) | 97.5 (1.3) | 1.1 (0.7) |
| N, Cα, C (fixed)4 | 3 | 0.06 (0.02) | 0.82 (0.11) | 89.4 (2.7) | 75.8 (4.5) | 2.07 (0.22) | 27.8 (8.6) | 97.9 (1.2) | 1.1 (0.7) |
| N, Cα, C, O | 4 | 0.04 (0.01) | 0.82 (0.11) | 89.6 (2.8) | 75.6 (4.7) | 2.08 (0.22) | 26.9 (8.3) | 97.4 (1.3) | 1.0 (0.8) |
| N, Cα, C, O (fixed) 4 | 4 | 0.00 (0.00) | 0.82 (0.11) | 89.7 (2.8) | 75.7 (4.6) | 2.05 (0.22) | 27.3 (8.3) | 97.9 (1.2) | 1.1 (0.8) |
|
| |||||||||
| CM5 | 1 | 0.22 (0.05) | 0.46 (0.06) | 95.4 (1.9) | 85.9 (3.9) | 2.00 (0.23) | 20.6 (6.2) | 97.3 (1.4) | 1.1 (0.7) |
| SC6 | 1 | 0.29 (0.07) | 0.49 (0.06) | 92.8 (2.4) | 85.6 (4.1) | 2.13 (0.28) | 22.9 (7.1) | 97.0 (1.5) | 1.5 (1.0) |
| Cα + CM5 | 2 | 0.11 (0.03) | 0.39 (0.05) | 98.0 (1.3) | 88.7 (3.6) | 1.97 (0.20) | 22.7 (6.8) | 97.7 (1.2) | 0.8 (0.7) |
| Cα + CM5 (fixed) 4 | 2 | 0.10 (0.03) | 0.39 (0.05) | 98.0 (1.3) | 88.8 (3.5) | 1.99 (0.21) | 23.6 (6.9) | 97.7 (1.2) | 0.8 (0.7) |
| Cα + SC6 | 2 | 0.13 (0.04) | 0.40 (0.04) | 95.2 (1.9) | 88.9 (3.4) | 1.93 (0.21) | 20.1 (6.2) | 97.7 (1.2) | 0.9 (0.7) |
| Cα + SC6 (fixed) 4 | 2 | 0.12 (0.04) | 0.39 (0.04) | 95.1 (1.9) | 89.1 (3.4) | 1.96 (0.21) | 21.4 (6.3) | 97.6 (1.2) | 0.9 (0.7) |
| MARTINI | 5 | 0.08 (0.02) | 0.31 (0.05) | 98.8 (1.0) | 93.1 (2.8) | 1.88 (0.21) | 17.2 (5.4) | 97.5 (1.2) | 0.9 (0.7) |
| PRIMO | 8 | 0.04 (0.01) | 0.18 (0.03) | 99.9 (0.2) | 99.7 (0.5) | 1.72 (0.27) | 10.7 (4.2) | 97.5 (1.3) | 1.1 (0.9) |
The average reconstruction accuracy measures for the test set protein structures (n=720) are given with their standard deviations in the parentheses.
Side chain χ-angles were considered accurate when deviations from experimental values were less than 30 degrees.
Experimental structures were reconstructed with the rigid body blocks using residue orientations and torsion angles from the experimental structures.
The atomic coordinates in the input files were preserved, while the original method does not. For instance, cg2all model for “Cα (fixed)” generates output structures with the exact same Cα coordinates of the input structures. On the other hand, the original cg2all model generates slightly altered Cα coordinates.
A bead located at the center-of-mass of an amino acid.
A bead located at the center-of-mass of sidechain atoms. For glycine, it is located at the position of Cα atom.