Table 7 Gibbs free energies
From: Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
Energy of the protein | Energy protein-solvent | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Class | Model | Nres | E 0 |
| σ E | E 0 |
| σ E | TS | G* |
|
all-α | NS0 | 105 | -5 739 | -5 316 | 345 | -18 266 | -17 123 | 672 | 1 157 | -23 596 | -24 019 |
ST1 | 105 | -4 002 | -4 536 | 424 | -20 587 | -18 616 | 827 | 1 245 | -24 397 | -23 863 | |
ST2 | 91 | -4 719 | -4 892 | 335 | -15 330 | -15 354 | 636 | 1 119 | - | - | |
ST3 | 104 | -3 041 | -4 745 | 543 | -21 442 | -17 646 | 1 026 | 1 325 | -23 716 | -22 012 | |
DT1 | 105 | -2 379 | -4 627 | 400 | -23 278 | -17 894 | 798 | 1 483 | -24 004 | -21 756 | |
DT2 | 105 | -5 018 | -5 755 | 289 | -16 742 | -15 625 | 509 | 1 337 | -22 717 | -21 980 | |
all-β | NS0 | 106 | -6 018 | -5 159 | 383 | -15 237 | -15 023 | 757 | 1 193 | -21 375 | -22 448 |
ST1 | 106 | -3 932 | -4 836 | 333 | -18 562 | -15 585 | 657 | 1 274 | -21 695 | -23 768 | |
ST2 | 104 | -2 828 | -3 651 | 404 | -18 910 | -16 835 | 779 | 1 315 | -21 801 | -23 053 | |
DT1b | 98 | -3 068 | -3 621 | 355 | -17 127 | -15 244 | 681 | 1 368 | - | - | |
DT1a | 112 | -3 301 | -5 385 | 468 | -19 417 | -15 484 | 843 | 1 304 | - | - | |
DT2 | 106 | -3 483 | -4 426 | 374 | -18 988 | -16 233 | 704 | 1 185 | -21 844 | -23 656 | |
αβ | NS0 | 260 | -16 963 | -13 912 | 452 | -28 307 | -30 284 | 826 | 2 339 | -46 535 | -49 586 |
ST1 | 260 | -11 223 | -11 888 | 503 | -36 671 | -33 328 | 991 | 2 534 | -47 750 | -47 085 | |
ST2 | 260 | -6 735 | -9 817 | 911 | -42 134 | -36 954 | 1 625 | 2 731 | -49 502 | -46 420 | |
ST3 | 200 | -6 774 | -8 629 | 445 | -28 844 | -25 728 | 790 | 2 104 | - | - | |
DT1 | 196 | -2 578 | -5 515 | 907 | -40 953 | -34 756 | 1 653 | 2 382 | - | - | |
DT2 | 260 | -8 369 | -10 391 | 655 | -40 331 | -35 703 | 1 145 | 2 716 | -48 810 | -46 788 | |