Biology Reference
In-Depth Information
2. Ma J, Karplus M. (1998). The allosteric mechanism of the chaperonin GroEL:
a dynamic analysis
. Proc Natl Acad Sci USA
95
: 8502-7.
3. Dal Peraro M, Ruggerone P, Raugei S
et al
. (2007) Investigating biological
systems using first principles Car-Parrinello molecular dynamics simulations
.
Curr Opin Struct Biol
17
: 149-56.
4. van Vlijmen HW, Schaefer M, Karplus M. (1998) Improving the accuracy of
protein pKa calculations: conformational averaging versus the average structure
.
Proteins
33
: 145-58.
5. Morea V, Lesk AM, Tramontano A. (2000) Antibody modeling: implications for
engineering and design
. Methods
20
: 267-79.
6. Liu Y, Gray NS. (2006). Rational design of inhibitors that bind to inactive kinase
conformations
. Nat Chem Biol
2
: 358-64.
7. Alder BJ, Wainwright TE. (1957) Phase transition for hard sphere systems
.
J Chem Phys
27
: 1208.
8. Alder BJ, Wainwright TE. (1959) Studies in molecular dynamics. I. General
method
. J Chem Phys
31
: 459.
9. Rahman A. (1964) Correlations in the motion of atoms in liquid argon
.
Phys Rev A
136
: 405-11.
10. Stillinger FH, Rahman A. (1974) Improved simulation of liquid water by molec-
ular dynamics.
J Chem Phys
60
: 1545-57.
11. McCammon JA, Gelin BR, Karplus M. (1977) Dynamics of folded proteins
.
Nature
267
: 585-90.
12. Darden T, Perera L, Li L, Pedersen L. (1999) New tricks for modelers from the
crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic
acid simulations
. Structure
7
: R55-60.
13. Lamoureux G, Roux B. (2006) Absolute hydration free energy scale for
alkali and halide ions established from simulations with a polarizable force field
.
J Phys Chem B
110
: 3308-22.
14. Olsen L, Rydberg P, Rod TH, Ryde U. (2006) Prediction of activation
energies for hydrogen abstraction by cytochrome p450
. J Med Chem
49
:
6489-99.
15. Dinner AR, Blackburn GM, Karplus M. (2001) Uracil-DNA glycosylase acts by
substrate autocatalysis
. Nature
413
: 752-5.
16. Chandler D. (1987).
Introduction to Modern Statistical Mechanics.
New York,
NY: Oxford University Press.
17. Hoover WG. (1985) Canonical dynamics: equilibrium phase-space distributions
.
Phys Rev A
31
: 1695.
18. Tuckerman ME, Liu Y, Ciccotti G, Martyna GJ. (2001) Non-Hamiltonian
molecular dynamics: generalizing Hamiltonian phase space principles to non-
Hamiltonian systems
. J Chem Phys
115
: 1678.
19. Huenenberger PH. (2005) Thermostat algorithms for molecular dynamics
simulations
. Adv Polym Sci
173
: 105.