In Suk Joung, and T.E. Cheatham, III. "Determination of alkali
and halide monovalent ion parameters for use in explicitly solvated
biomolecular simulations." J. Phys. Chem. B
(2008). [in press, ASAP].
[
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JPCB
ASAP link + Supplementary Material
]
H. Wang, T.E. Cheatham, III, and J. Lewis. "Differential electronic states observed during the A-B DNA duplex conformational transitions." Soft Matter (2008). [submitted].
S. S. Pendley, Y. B. Yu, and T.E. Cheatham, III. "Molecular
dynamics guided study of salt bridge length dependence in both
fluorinated and non-fluorinated parallel dimeric coiled-coil
proteins." Proteins (2008) [in press].
[
local PDF of proofs]
D. Svozil, J.E. Sponer, I. Marchan, A. Perez, T.E. Cheatham, III,
J. Luque, M. Orozco, and J. Sponer. "Geometrical and electronic
structure variability of the sugar-phosphate backbone in nucleic
acids." J. Phys. Chem. B 112, 8188-8197 (2008).
[
local PDF:
JPCB
link + Supplementary Material
]
A. Perez, I. Marchan, D. Svozil, J. Sponer, T.E. Cheatham, III,
C.A. Laughton, M. Orozco. "Refinement of the AMBER force field for
nucleic acids. Improving the description of alpha/gamma conformers."
Biophys. J. 92, 3817-3829 (2007).
[
local PDF:
BJ link
]
A. Wierzbicki, P. Dalal, T.E. Cheatham, III, J.E. Knickelbein,
A.D.J. Haymet, and J.D. Madura. "Antifreeze proteins at the ice/water
interface: Three calculated discriminating properties for orientation
of type I proteins." Biophys. J. 93, 1442-1451 (2007).
[
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BJ link
]
J. Shao, S. W. Tanner, N. Thompson, T.E. Cheatham, III. "Clustering
molecular dynamics trajectories: I. Characterizing the performance of
different clustering algorithms." J. Chem. Theory Comp. 3,
2312-2334 (2007).
[
local PDF:
ACS Link
+ Supporting info
]
P. Auffinger, T.E. Cheatham, III, and A. C. Vaiana. "Spontaneous
formation of KCl aggregates in biomolecular simulations: a force field
issue?." J. Chem. Theory Comp. 3, 1851-1859 (2007).
[
local PDF:
ACS Link
+ Supporting info
]
T.E. Cheatham, III and D.A. Case. "Using AMBER to simulate DNA and
DNA" in Computational Studies of DNA and RNA (Wiley) Editors,
J. Sponer and F. Lankas p. 45-72.
[
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N. Spackova, T.E. Cheatham, III and J. Sponer. "Molecular dynamics simulations of nucleic acids" in Computational Studies of DNA and RNA (Wiley) Editors, J. Sponer and F. Lankas p. 301-326.
F. Paesani, W. Zhang, D.A. Case, T.E. Cheatham, III and G.A. Voth. "An
accurate and simple quantum model for liquid water."
J. Chem. Phys. 125, 184507 (2006).
[
local PDF:
JCP link
]
T.N. Truong, M. Nayak,H. Huynh, T. Cook, P. Marajan, L.T. Tran,
J. Bharath, S. Jain, H.B. Pham, N. Nguyen, Y. Kim, S. Choe,
T.E. Cheatham, III, and J. Facelli, "Computational Science and
Engineering Online (CSE-Online): A cyberinfrastructure for scientific computing."
J. Chem. Info. Mod. 46, 971-984 (2006).
[
local PDF:
ACS link
]
T. E. Cheatham, III ''Molecular modeling and atomistic simulation of
nucleic acids.''
Ann. Reports Comp. Chem. Editor: D. Spellmeyer, Vol 1, pp. 75-89.
[
local PDF]
D. A. Case, T.E. Cheatham, III, T.A. Darden, H. Gohlke, R. Luo,
K. M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang, and
R. Woods. "The AMBER biomolecular simulation programs."
J. Comp. Chem. 26, 1668-1688
[
local PDF:
JCC link
]
S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham III,
E. Giudice, F. Lankas, R. Lavery, J. Maddocks, R. Osman, H. Sklenar,
K.M. Thayer, and P. Varnai. "Molecular dynamics simulations of the 136
unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence
context effects on the dynamical structures of the 10 unique
dinucleotide steps." Biophys. J. 89, 3721-3740.
[
local PDF:
BJ link
]
D. L. Beveridge, G. Barreiro, K. S. Byun, D. A. Case, T. E. Cheatham,
III, S. B. Dixit, E. Guidice, F. Lankas, R. Lavery, J. Maddocks,
R. Osman, H. Sklenar, G. Stoll, K. M. Thayer, P. Varnai, and
M. A. Young, ``Molecular dynamics simulations of the 136 unique
tetranucleotide sequences of DNA oligonucleotides. I. Research design,
informatics, and results on d(CpG) steps,'' Biophys. J. 87, 3799-3813.
[
local PDF:
BJ link
]
T. E. Cheatham, III ''Simulation and modeling of nucleic acid
structure, dynamics and interactions.''
Curr. Opin. Struct. Biol. 14, 360-367 (2004)
[
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F. Lankas, J. Sponer, J. Langowski, and T. E. Cheatham, III. ''DNA
deformability at the base pair level.''. J. Amer. Chem. Soc.
126, 4124-4125 (2004).
[
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PubMed:
JACS:
WOS]
E. Fadrna, N. Spackova, R. Stefl, J. Koca, T. E. Cheatham, III, and
J. Sponer. ''Molecular dynamics simulations of guanine quadruplex
loops: Advances and force field limitations''. Biophys. J. 87, 227-242
(2004)].
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N. Spackova, T. E. Cheatham, III, F. Ryjacek, F. Lankas, L. van
Meervelt, P. Hobza, and J. Sponer. ''Molecular dynamics simulations
and thermodynamics analysis of DNA-drug complexes. Minor groove
binding between 4.-6-diamino-2-phenylindole and DNA duplexes in
solution''. J. Amer. Chem. Soc. 125, 1759-1769 (2003).
[
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PubMed:
JACS:
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]
R. Stefl, T. E. Cheatham, III, N. Spackova, E. Fadrna, I. Berger,
J. Koca, and J. Sponer. ``Formation pathways of a guanine-quadruplex DNA
revealed by molecular dynamics and thermodynamical analysis of the
substates''. Biophys. J. 85, 1787-1804 (2003).
[
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Biophys J:
WOS
]
J. P. Lewis, T. E. Cheatham, III, H. Wang, E. Starikow, and
O. F. Sankey. ``Dynamically amorphous character of electronic states in
poly(dA)-poly(dT) DNA''. J. Phys. Chem. B 107, 2581-2587 (2003).
[
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JPC B:
WOS
]
F. Lankas, J. Sponer, J. Langowski & T. E. Cheatham, III. ``DNA
base-pair step deformability inferred from molecular dynamics
simulation''. Biophys. J. 85, 2872-2883 (2003)
[
local PDF:
PubMed:
Biophys J
]
F. Lankas, T. E. Cheatham, III, P. Hobza, J. Langowski,
N. Spackova, and J. Sponer. ``Critical effect of the N2 amino group on
structure, dynamics and elasticity of DNA polypurine
tracts''. Biophys. J. 82, 2592-2609 (2002).
[
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PubMed:
Biophys J:
WOS
]
J. P. Lewis, J. Pikus, T. E. Cheatham, III, E. B. Starikov,
H. Wang, J. Tomfohr, and O. F. Sankey. ``A comparison of electronic
states in periodic and aperiodic poly(dA)-poly(dT) DNA''.
Phys. Stat. Sol. (b) 233, 90-100 (2002).
[
local PDF:
Wiley:
WOS
]
T. E. Cheatham, III and M. A. Young. ``Molecular dynamics
simulations of nucleic acids: Successes, limitations and promise''.
Biopolyers Nuc. Acid Sci. 56, 232-256 (2001).
[
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Biopolymers:
WOS
]
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. ``Molecular modeling of nucleic acid structure: Energy and sampling'' in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.8.1-7.8.21 (2001)
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. ``Molecular modeling of nucleic acid structure: Electrostatics and solvation'' in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.9.1-7.9.22 (2001).
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. ``Molecular modeling of nucleic acid structure: Setup and analysis'' in Current Protocols in Nucleic Acid Chemistry. (Wiley: New York) 7.10.1-7.10.18 (2001).
T. E. Cheatham, III & P. A. Kollman. ``Molecular dynamics simulations
of nucleic acids'' in Ann. Rev. Phys. Chem. 51, 434-471
(2000).
[
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Ann Rev Phys Chem:
WOS
]
T. E. Cheatham, III, B. R. Brooks & P. A. Kollman. ``Molecular modeling of nucleic acid structure'' in Current Protocols in Nucleic Acid Chemistry1: 7.5.1-7.5.12. Wiley: New York (2000).
P. A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong,
M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak,
J. Srinivasan, D. A. Case & T. E. Cheatham, III. ``Calculating
structures and free energies of complex molecules: Combining molecular
mechanics and continuum models.'' Acc. Chem. Res. 33, 889-897 (2000).
[
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PubMed:
Acc Chem Res:
WOS
]
T. E. Cheatham, P. Cieplak & P. A. Kollman.
``A modified version of the Cornell et al. force field with improved
sugar pucker phases and helical repeat.''
J. Biomol. Struct. Dyn. 16, 845-862 (1999).
[
local PDF:
PubMed:
WOS
]
D. E. Konerding, T. E. Cheatham, III, P. A. Kollman & T. L. James.
``Restrained molecular dynamics of solvated duplex DNA using the
particle mesh Ewald method'' J. Biomol. NMR. 13, 119-131 (1999).
[
local PDF:
PubMed:
J Biomol NMR
]
J. L. Miller, T. E. Cheatham, III, & P. A. Kollman. "Simulation of Nucleic Acid Structure." Oxford Handbook of Nucleic Acid Structure S. Neidle, editor; Oxford University Press, pp. 95-115 (1999).
M. F. Crowley, T. A. Darden, T. E. Cheatham, III & D. Deerfield. "Fine- and coarse-grain parallel AMBER and particle mesh Ewald on MPP's" in Parallel Computing for Industrial and Scientific Applications, Eds: J. Jenness (Morgan-Kaufmann) (1999).
T. E. Cheatham, III & B. R. Brooks.
``Recent advances in molecular dynamics simulation towards realistic
representation of biomolecules in solution".
Theor. Chem. Acc. 99, 279-288 (1998).
[
local PDF:
SpringerLink:
WOS
]
T. E. Cheatham, J. Srinivasan, D. A. Case & P. A. Kollman.
``Molecular dynamics and continuum solvent studies of the stability
of polyG-polyC and polyA-polyT DNA duplexes in solution.''
J. Biomol. Struct. Dyn. 16, 265-280 (1998).
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]
T. E. Cheatham, III & P. A. Kollman. ``Molecular dynamics simulation
of nucleic acids in solution: How sensitive are the results to small
perturbations in the force field and environment?'' in Structure,
Motion, Interactions and Expression of Biological Macromolecules,
Proceedings of the 10th Conversation. Eds: R.H. Sarma & M.H. Sarma
(Adenine Press) p. 99-116 (1998).
[
local PDF
]
T. E. Cheatham, III, J. L. Miller, T. I. Spector, P. Cieplak & P. A. Kollman. ``Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics.'' in Modeling and Structure Determination of Nucleic Acids. Eds: N.B. Leontis & J. Santa Lucia Jr (ACS: Washington, DC) p. 285-303 (1998).
S. Bogusz, T. E. Cheatham, III & B. R. Brooks.
``Removal of pressure and free energy artifacts in charged periodic systems
via net charged corrections to the Ewald potential.''
J. Chem. Phys. 108, 7070-7084 (1998).
[
WOS
]
J. Srinivasan, T. E. Cheatham, III, P. Cieplak, P. A. Kollman &
D. A. Case. ``Continuum solvent studies of the stability of DNA, RNA
and phosphoramidate-DNA helices.'' J. Amer. Chem. Soc. 120, 9401-9409
(1998).
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JACS:
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]
S. C. Harvey, R. K.-Z. Tan & T. E. Cheatham, III.
``The flying ice cube: Velocity rescaling in molecular dynamics leads to
violation of energy equipartition.''
J. Comp. Chem.19, 726-740 (1998).
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local PDF:
JCC:
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]
P. A. Kollman, D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, III, S. DeBolt, D. M. Ferguson & G . Seibel. ``AMBER'' in Encyclopedia of Computational Chemistry Wiley-Interscience:NY (1998).
M. Hodoscek, E. M. Billings, T. E. Cheatham, III & B. R. Brooks. ``High performance computing in biophysics: Recent experiences and developments of CHARMM.'' Proceedings of the International Symposium on Supercomputing: New Horizons of Computational Science. Kluwer Academic (1998).
T. E. Cheatham, III, J. L. Miller, T. I. Spector, P. Cieplak & P. A. Kollman. ``Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics.'' in Modeling and Structure Determination of Nucleic Acids, ACS Symposium Series No. 682. Leontis, NB & Santa Lucia, Jr J, editors. p 285-303 (1998).
T.E. Cheatham, III & P.A. Kollman.
``Insight into the stabilization of A-DNA by specific ion
association: Spontaneous B-DNA to A-DNA transitions observed in molecular
dynamics simulations of d[ACCCGCGGGT]2 in the presence of
hexaamminecobalt(III).''
Structure 5, 1297-1311 (1997).
[
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PubMed:
Structure:
WOS
]
T.E. Cheatham, III, M.F. Crowley, T. Fox & P.A. Kollman.
``A molecular level picture of the stabilization of A-DNA in mixed
ethanol-water solutions''
Proc. Natl. Acad. Sci. 94, 9626-9630 (1997).
[
local PDF:
PubMed:
PNAS:
PubMed Central
]
T.E. Cheatham, III & P. A. Kollman.
``Molecular dynamics simulations highlight the
structural differences among DNA:DNA, RNA:RNA and
DNA:RNA hybrid duplexes''
J. Amer. Chem. Soc. (1997) 119 4805-4825.
[
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JACS:
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]
P. Cieplak, T.E. Cheatham, III & P.A. Kollman.
``Molecular dynamics simulations find that 3' phosphoramidate
modified DNA duplexes undergo a B to A transition and normal DNA
duplexes an A to B transition.''
J. Amer. Chem. Soc. 119, 6722-6730 (1997).
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]
T. Spector, T. E. Cheatham, III & P.A. Kollman.
``Unrestrained molecular dynamics of photodamaged DNA in aqueous solution.''
J. Amer. Chem. Soc. 119, 7095-7104 (1997).
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]
M. F. Crowley, T. A. Darden, T. E. Cheatham, III & D. Deerfield.
``Adventures in improving the scaling and accuracy of a parallel
molecular dynamics program.'' J. Supercomputing 11(3),
255-278 (1997)
[
WOS
]
T. A. Darden, L. G. Pedersen, A. Y. Toukmaji, M. F. Crowley & T. E. Cheatham, III. ``Particle-mesh based methods for fast Ewald summation in molecular dynamics simulations''. Proceedings of the Eighth SIAM Conference on Parallel Processing for Scientific Computing. M. Heath et al., editors. Minn, MN. March (1997).
T.E. Cheatham, III & P.A. Kollman.
``Observation of the A DNA to B DNA transition during
unrestrained molecular dynamics in aqueous solution.''
J. Mol. Biol. 259:(3), 434-444 (1996).
[
local PDF:
PubMed:
DOI
]
T.E. Cheatham, III, J.L. Miller, T. Fox, T.A. Darden and
P.A. Kollman. ``Molecular dynamics simulations on solvated
biomolecular systems: The Particle Mesh Ewald method leads to
stable trajectories of DNA, RNA, and proteins.''
J. Amer. Chem. Soc. 117, 4193 (1995).
[
local PDF:
JACS
]
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross,
T.E. Cheatham III, S. DeBolt, D.M. Ferguson,
G.L. Seibel and P.A. Kollman. ``AMBER, a package of computer
programs for applying molecular mechanics, normal mode
analysis, molecular dynamics and free energy calculations to
simulate the structural and energetic properties of molecules.''
Computer Physics Communications, 91, 1-41. (1995)
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