Publications
E-mail tec3@utah.edu for access to the local PDF links!
2013
TE Cheatham, III and D.A. Case. "Twenty-five years of nucleic acid simulations."Biopolymers [in press] (2013).
D Roe and TE Cheatham, III. "PTRAJ and CPPTRAJ: Software for
processing and analysis of molecular dynamics trajectory
data." J. Chem. Theory Comp. [in press] (2013).
...the long awaited PTRAJ paper!
[DOI: 10.1021/ct300671y]
J Sponer, A Mladek, N Spackova, X Cang, TE Cheatham, III and S. Grimme. "Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations." J. Amer. Chem. Soc. [in press] (2013).
M Zgarbova, F Javier Luque, J Sponer, TE Cheatham, III,
M Otyepka, and P Jurecka. "Toward improved description of DNA
backbone: Revisiting epsilon and zeta torsion force field
parameters." J. Chem. Theory Comp. 9, 2339-2354 (2013).
[
local PDF:
JCTC link
]
P Stadlbauer, M Krepl, TE Cheatham, III, J Koca and
J. Sponer. "Structural dynamics of possible late-stage intermediates
in folding quadruplex DNA studied by molecular simulations."
Nuc. Acids Res. [in press] (2013).
[
local PDF:
NAR link
]
NM Henriksen, DR Roe, and TE Cheatham, III. "Reliable oligonucleotide
conformational ensemble generation in explicit solvent for force field
assessment using reservoir replica exchange molecular dynamics simulations."
J. Phys. Chem. B [ASAP] (2013).
[
local PDF:
JPCB link
]
JC Thibault, JC Facelli, and TE Cheatham, III. "iBIOMES: Managing and
sharing biomolecular simulation data in a distributed environment."
J. Chem. Info. Model. [ASAP] (2013).
[
local PDF:
JCIM link
]
2012
NM Henriksen, DR Davis, and TE Cheatham, III. "Molecular dynamics
re-refinement of two different small RNA loop structures using the
original NMR data suggest a common structure." J. Biomol. NMR
53, 321-339 (2012).
[
local PDF:
J. Biomol. NMR link
]
M Krepl, M Zgarbova, P. Stadlbauer, M Otyepka, P Banas, J Koca, TE
Cheatham, IIII, P Jurecka, and J Sponer. "Reference simulations of
noncanonical nucleic acids with different chi variants of the AMBER
force field: Quadruplex DNA, quadruplex RNA, and Z-DNA."
J. Chem. Theory Comp. 8, 2506-2520 (2012).
[
local PDF:
JCTC link
]
J Sponer, X Cang, and TE Cheatham, III. "Molecular dynamics
simulations of G-DNA and perspectives on the simulation of nucleic
acid structures." Methods (2012) [ASAP].
[
local PDF:
Methods link
]
DL Beveridge, TE Cheatham, III, and M Mezei. "The ABCs of molecular
dynamics simulations on B-DNA, circa 2012." J. Bioscience
37, 379-397 (2012).
[
local PDF:
J Bioscience link
]
K Shahrokh, TE Cheatham, III, and GS Yost. "Conformational
dynamics of CYP3A4 demonstrate the important role of Arg212 coupled
with the opening of ingress, egress and solvent channels to
dehydrogenation of 4-hydroxy-tamoxifen."
Biochem. Biophys. Acta. 1820, 1605-1617 (2012) [ASAP].
[
local PDF:
BBA link]
Z. Lin, M. Flores, I. Forteza, N.M. Henriksen, G.P. Concepcion,
G. Rosenberg, M.G. Haygood, B.M. Olivera, A.R. Light, T.E. Cheatham,
III and E.W. Schmidt. "Totopotensamides, Polyketide-Cyclic Peptide
Hybrids from a Mollusk-Associated Bacterium Streptomyces sp."
J. Nat. Prod. 75, 644-649 (2012).
[
local PDF:
JNP link]
A.S. Dixon, G.D. Miller, B.J. Bruno, J.E. Constance, D.W. Woessner,
T.P. Fidler, J.C. Robertson, T.E. Cheatham, III and C.S. Lim.
"Improved coiled-coil design enhances interaction with Bcr-Abl and
induces apoptosis."
Mol. Pharm. 9, 187-195 (2012)
[
local PDF:
Mol Pharm link:
!Correction! PDF]
K. Shahrokh, A. Orendt, G. S. Yost, and T. E. Cheatham, III. "Quantum mechanically
derived AMBER-compatible heme parameters for various states of the
cytochrome P450 catalytic cycle."
J. Comp. Chem. 33, 119-133 (2012).
[
local PDF:
JCC link
]
2011
X. Cang, J. Sponer, and T. E. Cheatham, III
"Insight into G-DNA structural polymorphism and folding from sequence
and loop connectivity through free energy analysis."
J. Amer. Chem. Soc. 133, 14270-14279 (2011).
[
local PDF:
JACS link
]
A. S. Dixon, S. S. Pendley, B. J. Bruno, D. W. Woessner, A. A. Shimpi,
T. E. Cheatham, III, and C. S. Lim. "Disruption of BCR-ABL coiled-coil
oligomerization by design." J. Biol. Chem. B 286. 27751-27760 (2011).
[
local PDF:
JBC link
]
M. Zgarbova, M. Otyepka, J. Sponer, A. Mladek, P. Banas, T. E. Cheatham,
III, and P. Jurecka. "Refinement of the Cornell et al. nucleic acid
force field based on reference quantum chemical calculations of
torsion profiles of the glycosidic torsion." J. Chem. Theory
Comp. 7, 2886-2902 (2011).
[
local PDF:
JCTC link
]
X. Wei, H. M. Henriksen, J. J. Skalicky, M. K. Harper, T.E. Cheatham,
III, C. M. Ireland, and R. M. Van Wagoner. "Araiosamines A-D:
Tris-bromoindole cyclic guanidine alkaloids from the marine sponge
clathria (Thalysias) araiosa."
J. Org. Chem. B 76, 5515-5523 (2011).
[
local PDF:
JOC link
]
K. C. Thomas, M. Ethirajan, K. Shakrokh, H. Sun, J. Lee,
T.E. Cheatham, III, G. S. Yost, and C. A. Reilly. "Structure-activity
relationships of capsaicin analogs and transient receptor potential
vanilloid 1-mediated human lung epithelia cell toxicity."
J. Pharmacol. Exp. Ther. 337, 400-410 (2011).
[
local PDF:
JPET link
]
X. Cang, J. Sponer, and T. E. Cheatham, III. "Explaining the varied
glycosidic conformational, G-tract length and sequence preferences for
anti-parallel G-quadruplexes." Nuc. Acids Res. 39, 4499-4512
(2011).
[
local PDF:
NAR link
]
R. DeMille, T. E. Cheatham, III, and V. Molinero. "A coarse-grained
model of DNA with explicit solvation by water and ions."
J. Phys. Chem. B 115, 132-142 (2011). PMC-3019136
[
local PDF:
JPC B link
]
2010
R. Lavery, K. Zakrzewska, D.L. Beveridge, T.C. Bishop, D.A. Case,
T.E. Cheatham, III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton,
J.H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh,
N. Spackova, and J. Sponer. "A systematic molecular dynamics study of
nearest-neighbor effects on base pair and base pair step conformations
and fluctuations in B-DNA." Nuc. Acids Res. 38, 299-313
(2010). PMCID: 2800215
[
local PDF:
NAR link
]
T. Truong, H. Freedman, L. Le, T.E. Cheatham, III, J. Tuszynski,
and L. Huynh. "Explicitly-solvated ligand contribution to continuum
solvation models for binding free energies: Selectivity of
theophylline binding to an RNA aptamer." J. Phys. Chem. B 114, 2227-2237 (2010).
[
local PDF:
JPCB link
]
R. B. Paulsen, P. P. Seth, E. E. Swayze, R. H. Griffey,
J. J. Skalicky, T. E. Cheatham, III, and D. R. Davis. "Inhibitor
induced structure change in the HCV IRES domain IIa RNA."
Proc. Natl. Acad. Sci. 107, 7263-7268 (2010).
[
local PDF:
PNAS link
]
C. D. Moore, K. Shahrokh, S. F. Sontum, T. E. Cheatham, III, and G. S. Yost.
"Improved Cyp3A4 molecular models accurately predict Phe215
requirement for raloxifene dehydrogentation selectivity."
Biochemistry 49, 9011-9019 (2010).
[
local PDF:
Biochemistry link
]
P. Banas, D. Hollas, M. Zgarbova, P. Jurecka, M. Orozco, T. E. Cheatham,
III, J. Sponer, and M. Otyepka. "Performance of molecular mechanics
force fields for RNA simulations. Stability of UUCG and GNRA
hairpins." J. Chem. Theory Comp. 6, 3836-3849 (2010).
[
local PDF:
JCTC link
]
K.F. Wong, J.L. Sonnerberg, F. Paesani, T. Yamamoto, J. Vanicek, J. Zhang,
H.B. Schlegl, D.A. Case, T.E. Cheatham, III, W.H. Miller, and G.A. Voth.
"Proton transfer studied using a combined ab initio reactive potential
energy surface with quantum path integral methodology."
J. Chem. Theory Comp. 6, 2566-2580 (2010).
[
local PDF:
JCTC link
]
2009
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 74, 612-629 (2009) [DOI:
10.1002/prot.22177] PMCID: 2692595.
[
local PDF:
Proteins link +
Supplementary Material
]
H. Wang, T.E. Cheatham, III, P.M. Gannett, and J. Lewis.
"Differential electronic states observed during the A-B DNA duplex
conformational transitions." Soft Matter 5, 685-690 (2009).
[
local PDF:
Soft Matter link
]
T. S. Han, M.-M. Zhang, A. Walewska, P. Gruszczynski, C.R. Robertson, T.E. Cheatham, III, D. Yoshikami, B. M. Olivera, and G. Bulaj. "Structurally-minimized .-conotoxin analogs as sodium channel blockers: Implications for designing conopeptide-based therapeutics." Chem. Med. Chem. 4, 406-414 (2009).
In Suk Joung, O. Persil Cetinkol, N. V. Hud, and T.E. Cheatham, III. "Molecular
dynamics simulations and coupled nucleotide substitution experiments
indicate the nature of A-A base pairing and a putative structure of
the coralyne-induced homo-adenine duplex." Nuc. Acids Res. 37,
7715-7727 (2009). PMCID: 2794157
[
local PDF:
NAR link
]
In Suk Joung, and T.E. Cheatham, III. "Molecular dynamics
simulations of the dynamic and energetic properties of alkali and
halide ions using water-model specific ion parameters."
J. Phys. Chem. B 113, 13279-13290 (2009). PMCID: 2755304
[
local PDF:
JPCB link +
Supplementary Material
]
E. Fadrna, N. Spackova, J. Sarzynska, J. Koca, M. Orozco,
T.E. Cheatham, III, T. Kulinski, J. Sponer. "Single stranded loops of
quadruplex DNA as key benchmark for testing nucleic acids force
field." J. Chem. Theory Comp. 5, 2514-2530 (2009).
[
local PDF:
JCTC link +
Supplementary Material
]
2008
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 112, 9020-9041 (2008).
[
local PDF:
JPCB link +
Supplementary Material
]
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
]
2007
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).
[
local PDF:
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
]
2006
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.
[
local PDF]
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
]
2005
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
]
2004
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)
[
local PDF]
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).
[
local PDF:
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)].
[
local PDF ]
2003
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).
[
local PDF:
PubMed:
JACS:
WOS
]
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).
[
local PDF:
PubMed:
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).
[
local PDF:
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
]
2002
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).
[
local PDF:
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
]
2001
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).
[
local PDF:
PubMed:
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)
[
local PDF:
Current Protocols link
]
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).
[
local PDF:
Current Protocols link
]
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).
[
local PDF:
Current Protocols link
]
2000
T. E. Cheatham, III & P. A. Kollman. ``Molecular dynamics simulations
of nucleic acids'' in Ann. Rev. Phys. Chem. 51, 434-471
(2000).
[
local PDF:
PubMed:
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).
[
local PDF:
Current Protocols link
]
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).
[
local PDF:
PubMed:
Acc Chem Res:
WOS
]
1999
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).
1998
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).
[
local PDF:
PubMed:
WOS
]
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).
[
local PDF:
JACS:
WOS
]
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).
[
local PDF:
JCC:
WOS
]
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).
1997
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).
[
local PDF:
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.
[
local PDF:
JACS:
WOS
]
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).
[
local PDF:
JACS:
WOS
]
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).
[
local PDF:
JACS:
WOS
]
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).
1996
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
]
1995
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)
[
local
PDF ]
