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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 E ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyrauKbaebaaaa@2CFE@ σ E E 0 E ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyrauKbaebaaaa@2CFE@ σ E TS G* G 0 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaem4raC0aa0baaSqaaiabicdaWaqaaiabgEHiQaaaaaa@2EF4@
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
  1. E0 is the energy for the initial conformation at t = 0; E ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyrauKbaebaaaa@2CFE@ is the mean energy along the trajectory at T = 300 K;σ E is the corresponding standard deviation. Column 3 is the number of residues in the model. Columns 4–6 correspond to the intramolecular protein energy, columns 7–9 correspond to the interaction energy of the protein with the solvent. Column 10 is the entropic contribution. Column 11, G* is the approximation of the Gibbs free energy (see text). Column 12, E ¯ MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGafmyrauKbaebaaaa@2CFE@ is similar to G* except that it is computed using the protein is similar to G term E0 instead of G 0 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaem4raC0aa0baaSqaaiabicdaWaqaaiabgEHiQaaaaaa@2EF4@ . The Gibbs free energy is not computed for models for which the number of residues differs by more than a couple of residues from the query sequence length. All figures are in kJ/mol.