Free-energy calculations - Theoretical Biophysics Group

More documents

Recommendations

Info

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
Page 1 and 2:
Free-energy calculations Measuring
Page 3 and 4:
Foreword Free-energy differences ca
Page 5 and 6:
Page 7 and 8:
Page 9 and 10:
Free-energy perturbation calculatio
Page 11 and 12:
6 JORGENSEN, RAVIMOHAN (1985) 7 SIM
Page 13 and 14:
Page 15 and 16:
Page 17 and 18:
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 27 and 28:
Page 29 and 30:
Page 31 and 32:
11 HUMMER ET AL. (1996) 12 HÜNENBE
Page 33 and 34:
Page 35 and 36:
15 KIRKWOOD (1935) Free-energy pert
Page 37 and 38:
16 PEARLMAN, KOLLMAN (1989) Free-en
Page 39 and 40:
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 47 and 48:
Page 49 and 50: 22 POHORILLE ET AL. (2010) Free-ene
Page 51 and 52: Free-energy perturbation calculatio
Page 55 and 56: protein + ligand 0 ∆ Aannihilatio
Page 57 and 58: 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 77 and 78: Foreword Free-energy differences ca
Page 79 and 80: Reaction coordinate-based free-ener
Page 99: Reaction coordinate-based free-ener
Page 107 and 108: Good practices Free-energy perturba
Page 109 and 110: References BENNETT, C. H. (1976): E
Page 111 and 112: References KARLSSON, R.;LARSSON, A.
show all

Free-energy calculations - Theoretical Biophysics Group

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?