Free-energy calculations - Theoretical Biophysics Group

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protein + ligand 0 ∆ Aannihilation protein + nothing ∆ Abinding ∆ A =0 ∆ Arestrain Free-energy perturbation calculations “Alchemical transformations” protein ... ligand 1 ∆ Aannihilation protein ... nothing Alternative route: Double annihilation of the ligand, ∆Abinding = ∆A 0 annihilation − ∆A1 annihilation This implies obtaining ∆A0 annihilation and ∆A1 annihilation in the thermodynamic cycle. FEP is the appropriate technique, which, however, some care. Chris Chipot Free-energy calculations
protein + ligand 0 ∆ Aannihilation protein + nothing ∆ Abinding ∆ A =0 ∆ Arestrain Free-energy perturbation calculations “Alchemical transformations” protein ... ligand 1 ∆ Aannihilation protein ... nothing 27 GILSON ET AL. (1997); HERMANS, WANG (1997); DIXIT, CHIPOT (2001) 28 DENG, ROUX (2009) The ligand in the binding pocket is annihilated from a strongly constrained position, whereas the free, unbound ligand can translate, rotate and isomerize freely during annihilation. This means that the thermodynamic cycle reflecting micro-reversibility of the transformations may not zero out unless proper corrections for the loss of translational, rotational and conformational entropies are taken into account. 27 Under favorable circumstances, these corrections can be evaluated analytically. 28 Chris Chipot Free-energy calculations
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Free-energy calculations Measuring
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Foreword Free-energy differences ca
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Page 9 and 10: Free-energy perturbation calculatio
Page 11 and 12: 6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 19 and 20: 8 WIDOM (1963) Free-energy perturba
Page 21 and 22: Substitute where Free-energy pertur
Page 23 and 24: Substitute where Free-energy pertur
Page 25 and 26: P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
Page 31 and 32: 11 HUMMER ET AL. (1996) 12 HÜNENBE
Page 35 and 36: 15 KIRKWOOD (1935) Free-energy pert
Page 37 and 38: 16 PEARLMAN, KOLLMAN (1989) Free-en
Page 41 and 42: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 43 and 44: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 45 and 46: (a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
Page 55: protein + ligand 0 ∆ Aannihilatio
Page 63 and 64: 33 BEUTLER ET AL. (1994) 34 ZACHARI
Page 67 and 68: 36 POHORILLE ET AL. (2010) 37 LU ET
Page 79 and 80: Reaction coordinate-based free-ener
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Good practices Free-energy perturba
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References BENNETT, C. H. (1976): E
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References KARLSSON, R.;LARSSON, A.
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Free-energy calculations - Theoretical Biophysics Group

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