Free-energy calculations - Theoretical Biophysics Group

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Reaction coordinate–based free-energy calculations Reversible unfolding of a short peptide 54 PARK ET AL. (2003) 55 HÉNIN, CHIPOT (2004); CHIPOT, HÉNIN (2005) Pulling of deca–alanine to investigate the equilibrium between the native, α–helical conformation and an ensemble of extended structures. Steered molecular dynamics and the application of the Jarzynski equality with a cumulant expansion: 54 exp[−β ∆A(ξ)] = 〈exp[−β w(ξ)]〉 Reference reversible pulling: 200.0 ns Jarzynski: 100 × 2.0 ns (v = 10.0 ˚A/ns) 100 × 0.2 ns (v = 100.0 ˚A/ns) Unconstrained dynamics with the formalism of the average force. The chosen order parameter, ξ, is the distance separating the first and the last α–carbon atoms. 55 Chris Chipot Free-energy calculations
Reaction coordinate–based free-energy calculations Reversible unfolding of a short peptide 54 PARK ET AL. (2003) 55 HÉNIN, CHIPOT (2004); CHIPOT, HÉNIN (2005) Pulling of deca–alanine to investigate the equilibrium between the native, α–helical conformation and an ensemble of extended structures. Steered molecular dynamics and the application of the Jarzynski equality with a cumulant expansion: 54 exp[−β ∆A(ξ)] = 〈exp[−β w(ξ)]〉 Reference reversible pulling: 200.0 ns Jarzynski: 100 × 2.0 ns (v = 10.0 ˚A/ns) 100 × 0.2 ns (v = 100.0 ˚A/ns) Unconstrained dynamics with the formalism of the average force. The chosen order parameter, ξ, is the distance separating the first and the last α–carbon atoms. 55 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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Free-energy perturbation calculatio
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6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
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8 WIDOM (1963) Free-energy perturba
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Substitute where Free-energy pertur
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Substitute where Free-energy pertur
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P(∆U ) 2.4 2.0 1.6 1.2 0.8 P (∆
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11 HUMMER ET AL. (1996) 12 HÜNENBE
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15 KIRKWOOD (1935) Free-energy pert
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16 PEARLMAN, KOLLMAN (1989) Free-en
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(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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(a) 2.4 P(∆U ) 2.0 1.6 1.2 0.8 P
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Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
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Page 57 and 58: protein + ligand 0 ∆ Aannihilatio
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Page 109 and 110: References BENNETT, C. H. (1976): E
Page 111 and 112: References KARLSSON, R.;LARSSON, A.
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