Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 88

101. Westhof E. A tale in molecular recognition: the hammerhead ribozyme. J Mol Recognit.
2007;20:1-3.
102. Mayaan E, Moser A, MacKerell Jr AD, York DM. CHARMM force field parameters
for simulation of reactive intermediates in native and thio-substituted ribozymes.
J Comput Chem. 2007;28:495-507.
103. Foloppe N, MacKerell Jr AD. All-atom empirical force field for nucleic acids:
I Parameter optimization based on small molecule and condensed phase macromolec-
ular target data. J Comput Chem. 2000;21:86-104.
104. MacKerell Jr AD, Banavali NK. All-Atom empirical force field for nucleic Acids: II.
application to molecular dynamics simulations of DNA and RNA in solution.
J Comput Chem. 2000;21:105-120.
105. Nam K, Cui Q, Gao J, York DM. Specific reaction parametrization of the AM1/d
Hamiltonian for phosphoryl transfer reactions: H, O, and P atoms. J Chem Theory
Comput. 2007;3:486-504.
106. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M.
Charmm: a program for macromolecular energy minimization and dynamics calcula-
tions. J Comput Chem. 1983;4:187-217.
107. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of
simple potential functions for simulating liquid water. J Chem Phys. 1983;79:

926-935.
108. Andersen HC. Molecular dynamics simulations at constant pressure and/or tempera-
ture. J Chem Phys. 1980;72:2384-2393.
109. Hoover WG. Canonical dynamics: equilibration phase-space distributions. Phys Rev A .
1985;31:1695-1697.
110. Nose S, Klein ML. Constant pressure molecular dynamics for molecular systems. Mol
Phys. 1983;50:1055-1076.
111. Essmann U, Perera L, Berkowitz ML, Darden T, Hsing L, Pedersen LG. A smooth
particle mesh Ewald method. J Chem Phys. 1995;103:8577-8593.
112. Sagui C, Darden TA. Molecular dynamics simulations of biomolecules: long-range
electrostatic effects. Annu Rev Biophys Biomol Struct. 1999;28:155-179.
113. Allen MP, Tildesley DJ. Computer Simulation of Liquids. Oxford: Oxford University
Press; 1987.
114. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equa-
tions of motion of a system with constraints: molecular dynamics of n-Alkanes.
J Comput Phys. 1977;23:327-341.
115. Ponomarev SY, Thayer KM, Beveridge DL. Ion motions in molecular dynamics sim-
ulations on DNA. Proc Natl Acad Sci USA. 2004;101:14771-14775.
116. Hutter MC, Reimers JR, Hush NS. Modeling the bacterial photosynthetic reaction
center. 1. magnesium parameters for the semiempirical AM1 method developed using
a genetic algorithm. J Phys Chem B . 1998;102:8080-8090.
117. Gao J, Amara P, Alhambra C, Field MJ. A generalized hybrid orbital (GHO) method
for the treatment of boundary atoms in combined QM/MM calculations. J Phys Chem
A . 1998;102:4714-4721.
118. Nam K, Gao J, York DM. An efficient linear-scaling Ewald method for long-range
electrostatic interactions in combined QM/MM calculations. J Chem Theory Comput.
2005;1:2-13.
119. Lambert D, Heckman JE, Burke JM. Three conserved guanosines approach the
reaction site

in native and minimal hammerhead ribozymes. Biochemistry .

2006;45:7140-7147.
120. Boots JL, Canny MD, Azimi E, Pardi A. Metal ion specificities for folding and
cleavage activity in the Schistosoma hammerhead ribozyme. RNA .

2008;14:2212-2222.