Introduction to Molecular Dynamics: Theory and Applications in Biomolecular Modeling - Computational Modeling of Biological Systems - page 30

110. Swope, W.C., Andersen, H.C., Berens, P.H., Wilson, K.R.: A computer simulation method for
the calculation of equilibrium constants for the formation of physical clusters of molecules:
application to small water clusters. J. Chem. Phys. 76 , 637 (1982)
111. Tajkhorshid, E., Nollert, P., Jensen, M.Ø., Miercke, L.J.W., O'Connell, J., Stroud, R.M.,
Schulten, K.: Control of the selectivity of the aquaporin water channel family by global
orientational tuning. Science 296 , 525-530 (2002)
112. Teodoro, M.L., E., K.L.: Conformational flexibility models for the receptor in structure based
drug design 9 , 1419-1431 (2003)
113. Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E.,
Guvench, O., Lopes, P., Vorobyov, I., Jr., A.D.M.: CHARMM general force field: a force field
for drug-like molecules compatible with the CHARMM all-atom additive biological force
fields. J. Comp. Chem. 31 (4), 671-690 (2010)
114. Verlet, L.: Computer 'experiments' on classical fluids: I. Thermodynamical properties of
Lennard-Jones molecules. Phys. Rev. 159 , 98-103 (1967)
115. Voter, A.: Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys. Rev.
Lett. 78 , 3908-3911 (1997)
116. Voter, A.: A method for accelerating the molecular dynamics simulation of infrequent events.
J. Chem. Phys. 106 , 4665 (1997)
117. Wang, J., Cieplak, P., Kollman, P.: How well does a restrained electrostatic potential (RESP)
model perform in calculating conformational energies of organic and biological molecules?
J. Comp. Chem. 21 , 1049-1074 (2000)
118. Wang, J., Wang, W., Kollman, P.A., Case, D.A.: Automatic atom type and bond type
perception in molecular mechanical calculations. J. Mol. Graph. Model. 25 , 247-260 (2006)
119. Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of
a general AMBER force field. J. Comp. Chem. 25 , 1157-1174 (2004)
120. Wang, Y., Shaikh, S.A., Tajkhorshid, E.: Exploring transmembrane diffusion pathways with
molecular dynamics. Physiology 25 , 142-154 (2010)
121. Wereszczynski, J., McCammon, J.A.: Using selectively applied accelerated molecular dy-
namics to enhance free energy calculations. J. Chem. Theor. Comp. 6 , 3285-3292 (2010)
122. Williams, S., de Oliveira, C., McCammon, J.: Coupling constant ph molecular dynamics with
accelerated molecular dynamics. J. Chem. Theor. Comp. 6 , 560-568 (2010)
123. Wong, C., McCammon, J.: Protein flexibility and computer-aided drug design. Annu. Rev.
Pharm. Tox. 43 , 31 (2003)
124. Wong, C.F., McCammon, J.A.: Computer simulation and the design of new biological
molecules. Isr. J. Chem. 27 , 211-215 (1986)
125. Xu, D., Williamson, M., Walker, R.: Advancements in molecular dynamics simulations of
biomolecules on graphical processing units 6 , 2-19 (2010)
126. Zacharias, M., Straatsma, T., McCammon, J.: Separation-shifted scaling, a new scaling
method for Lennard-Jones interactions in thermodynamic integration. J. Chem. Phys. 100 ,
9025-9031 (1994)
127. Zhou, H.X., Gilson, M.K.: Theory of free energy and entropy in noncovalent binding. Chem.
Rev. 109 , 4092-4107 (2009)
128. Zhu, F., Tajkhorshid, E., Schulten, K.: Collective diffusion model for water permeation
through microscopic channels. Phys. Rev. Lett. 93 , 224,501 (2004). (4 pages)