| Table 5.1. Average energy values for the 33 proteins over varying s values. All energy values include valence and non-valence terms, and the units are presented in kcal/mol. The energies do not include interaction terms between atoms that are not involved in the sidechain placement calculations. Numbers in bold are the minimum values for each category. | ||||||||
|---|---|---|---|---|---|---|---|---|
|
s value |
0.6Å Library | 1.0Å Library | 1.4Å Library | All-Torsion Library | ||||
| Starting Energy |
Minimized Energy |
Starting Energy |
Minimized Energy |
Starting Energy |
Minimized Energy |
Starting Energy |
Minimized Energy |
|
| 0 | −1234.3 | −3163.1 | 546.8 | −2839.2 | 6957.0 | −2544.8 | 1558154.0 | −2317.1 |
| 0.2 | −2237.0 | −3225.5 | 530.7 | −2969.3 | 2804.0 | −2675.2 | 1260675.0 | −2515.2 |
| 0.4 | −2195.1 | −3271.3 | 417.6 | −3053.8 | 2610.3 | −2790.4 | 34774.5 | −2767.6 |
| 0.6 | −2364.8 | −3312.2 | −624.4 | −3102.8 | 3454.9 | −2871.2 | 34628.7 | −2826.2 |
| 0.8 | −2227.6 | −3328.1 | −419.9 | −3168.6 | 4970.1 | −2929.7 | 41225.3 | −2849.5 |
| 0.9 | −2130.1 | −3325.0 | −166.4 | −3165.1 | 10013.7 | −2941.8 | 166369.5 | −2836.7 |
| 1.0 | −2041.5 | −3331.6 | 143.2 | −3166.3 | 132017.6 | −2952.7 | 173157.0 | −2854.6 |
| 1.1 | −1952.9 | −3341.3 | 1431.4 | −3177.5 | 136424.5 | −2945.5 | 53846.7 | −2845.7 |
| 1.2 | −1764.6 | −3338.9 | 1885.2 | −3171.0 | 146372.5 | −2938.1 | 62057.7 | −2794.9 |
| 1.3 | −545.0 | −3327.5 | 3278.3 | −3161.9 | 161903.0 | −2919.4 | 101904.8 | −2783.0 |
| Table 5.2. Average RMSD values (inÅ) for the Xiang set of 33 proteins, before and after minimization. Entries in bold correspond to those with the lowest DREIDING energies before and after minimization, see Table 5.1 for details. | ||||||||
|---|---|---|---|---|---|---|---|---|
|
Scaling Factor |
0.6Å Library | 1.0Å Library | 1.4Å Library | All-Torsion Library | ||||
| Starting RMSD |
Minimized RMSD |
Starting RMSD |
Minimized RMSD |
Starting RMSD |
Minimized RMSD |
Starting RMSD |
Minimized RMSD |
|
| 0 | 0.830 | 0.737 | 1.036 | 0.930 | 1.171 | 1.061 | 1.112 | 1.003 |
| 0.2 | 0.784 | 0.694 | 0.954 | 0.848 | 1.071 | 0.962 | 1.035 | 0.916 |
| 0.4 | 0.746 | 0.658 | 0.884 | 0.773 | 1.003 | 0.887 | 0.975 | 0.848 |
| 0.6 | 0.706 | 0.615 | 0.827 | 0.718 | 0.930 | 0.814 | 0.954 | 0.823 |
| 0.8 | 0.681 | 0.591 | 0.784 | 0.668 | 0.888 | 0.767 | 0.920 | 0.787 |
| 0.9 | 0.682 | 0.591 | 0.766 | 0.651 | 0.877 | 0.752 | 0.917 | 0.786 |
| 1.0 | 0.672 | 0.581 | 0.764 | 0.647 | 0.863 | 0.736 | 0.916 | 0.780 |
| 1.1 | 0.662 | 0.569 | 0.747 | 0.625 | 0.860 | 0.729 | 0.923 | 0.786 |
| 1.2 | 0.657 | 0.562 | 0.752 | 0.629 | 0.861 | 0.727 | 0.937 | 0.799 |
| 1.3 | 0.662 | 0.568 | 0.758 | 0.632 | 0.860 | 0.724 | 0.946 | 0.803 |