Biomedical Engineering Reference
In-Depth Information
90. de Oliveira, C., Hamelberg, D., McCammon, J.: Coupling accelerated molecular dynamics
methods with thermodynamic integration simulations. J. Chem. Theor. Comp. 4 , 1516-1525
(2008)
91. Oostenbrink, C., van Gunsteren, W.F.: Free energies of ligand binding for structurally diverse
compounds. Proc. Natl. Acad. Sci. USA 102 , 6750-6754 (2005)
92. Oostenbrink, C., Villa, A., Mark, A.E., Gunsteren, W.F.V.: A biomolecular force field based
on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5
and 53A6. J. Comp. Chem. 25 , 1656-1676 (2004)
93. Park, S., Schulten, K.: Calculating potentials of mean force from steered molecular dynamics
simulations. J. Chem. Phys. 120 , 5946-5961 (2004)
94. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel,
R.D., Kale, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comp. Chem. 26 ,
1781-1802 (2005)
95. Pohorille, A., Jarzynski, C., Chipot, C.: Good practices in free-energy calculations. J. Phys.
Chem. B 114 , 10,235-10,253 (2010)
96. Price, M., Ostrovsky, D., Jorgensen, W.L.: Gas-phase and liquid-state properties of esters,
nitriles, and nitro compounds with the OPLS-AA force field. J. Comp. Chem. 22 , 1340-1352
(2001)
97. Roux, B.: The calculation of the potential of mean force using computer simulations. Comput.
Phys. Comm. 91 , 275-282 (1995)
98. Roux, B.: Ion conduction and selectivity in K C channels. Annu. Rev. Biomol. Struc. Dyn. 34 ,
153-171 (2005)
99. Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: Numerical integration of the Cartesian
equations of motion of a system with constraints: molecular dynamics of n -alkanes. J. Comp.
Phys. 23 , 327-341 (1977)
100. Schames, J.R., Henchman, R.H., Siegel, J.S., Sotriffer, C.A., Ni, H., McCammon, J.A.:
Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47 , 1879-1881 (2004)
101. Schlick, T.: Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd edn.
Springer, New York (2010)
102. Schuler, L., Daura, X., van Gunsteren, W.: An improved GROMOS96 force field for aliphatic
hydrocarbons in the condensed phase. J. Comp. Chem. 22 , 1205-1218 (2001)
103. Shaw, D.E., Dror, R.O., Salmon, J.K., Grossman, J., Mackenzie, K.M., Bank, J.A., Young, C.,
Deneroff, M.M., Batson, B., Bowers, K.J., Chow, E., Eastwood, M.P., Ierardi, D.J., Klepeis,
J.L., Kuskin, J.S., Larson, R.H., Lindorff-Larsen, K., Maragakis, P., Moraes, M.A., Piana,
S., Shan, Y., Towles, B.: Millisecond-scale molecular dynamics simulations on Anton. pp.
39:1-39:11. ACM, New York, NY, USA (2009)
104. Shaw, D.E., Maragakis, P., Lindorff-Larsen, K., Piana, S., Dror, R.O., Eastwood, M.P., Bank,
J.A., Jumper, J.M., Salmon, J.K., Shan, Y., Wriggers, W.: Atomic-level characterization of
the structural dynamics of proteins. Science 330 , 341-346 (2010)
105. Sherman, W., Day, T., Jacobson, M.P., Friesner, R.A., Farid, R.: Novel procedure for modeling
ligand/receptor induced fit effects. J. Med. Chem. 49 , 534-553 (2005)
106. Shirts, M.R., Bair, E., Hooker, G., Pande, V.S.: Equilibrium free energies from nonequilibrium
measurements using maximum-likelihood methods. Phys. Rev. Lett. 91 , 140,601 (2003)
107. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., Berendsen, H.J.C.:
Gromacs: fast, flexible, and free. J. Comp. Chem. 26 , 1701-1718 (2005)
108. Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.:
Accelerating molecular modeling applications with graphics processors. J. Comp. Chem. 28 ,
2618-2640 (2007)
109. Summa, V., Petrocchi, A., Bonelli, F., Crescenzi, B., Donghi, M., Ferrara, M., Fiore, F.,
Gardelli, C., Gonzalez Paz, O., Hazuda, D., Jones, P., Kinzel, O., Laufer, R., Monteagudo, E.,
Muraglia, E., Nizi, E., Orvieto, F., Pace, P., Pescatore, G., Scarpelli, R., Stillmock, K., Witmer,
M., Rowley, M.: Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase
inhibitor for the treatment of HIV-AIDS infection. J. Med. Chem. 51 , 5843-5855 (2008)
Search WWH ::




Custom Search