Cheatham Group

Publications

E-mail tec3@utah.edu for access to the local PDF links!


Google Scholar link


2016

HS Hayatshahi, DR Roe, R Galindo-Murillo, KB Hall, and TE Cheatham, III. "Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in the GTPase-Associating Center RNA." J. Phys. Chem. B (2016) [in press]

HS Hayatshahi, C Bergonzo, and TE Cheatham III. "Investigating the ion dependence of the first unfolding step of GTPase-associating center ribosomal RNA." J. Biomol. Struct. Dyn. (2016) [in press]

Y Hao, E Pierce, D Roe, M Morita, JA McIntosh, V Agarwal, TE Cheatham III, EW Schmidt, and SK Nair. "Molecular basis of broad-substrate selectivity of a peptide prenyltransferase." PNAS 113, 14037-14042 (2016).
     [ local PDF: PNAS link ]

Z Heidari, DR Roe, R Galindo-Murillo, JB Ghasemi, and TE Cheatham III. "Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations." J. Chem. Inf. Model. 56, 1282-1291 (2016).
     [ local PDF: JCIM link ]

R Galindo-Murillo, JC Robertson, M Zgarbová, J Šponer, M Otyepka, P Jurečka, and TE Cheatham III. "Assessing the current state of Amber force field modifications for DNA." J. Chem. Theory Comp. 12, 4114-4127 (2016). DOI: 10.1021/acs.jctc.6b00186
     [ local PDF: JCTC link ]

JT Waters, X-J Lu, R Galindo-Murillo, JC Gumbart, HD Kim, TE Cheatham, III and SC Harvey. "Transitions of double-stranded DNA between the A- and B- forms." J. Phys Chem. B 120, 8449-8456 (2016)
     [ local PDF: JPC B link ]

R Galindo-Murillo, DR Davis and TE Cheatham, III. "Probing the influence of hypermodified residues within the tRNA3Lys anticodon stem loop interacting with the A-loop primer sequence from HIV-1." Biochemica Biophys. Acta 1860, 607-617 (2016).
     [ local PDF: BBA link ]


2015

M Zgarbova, J Sponer, M Otyepka, TE Cheatham, III, R Galindo-Murillo, and P Jurecka. "Refinement of the sugar-phosphate backbone torsion beta for the AMBER force fields improves the description of Z-DNA and B-DNA." J. Chem. Theory Comp. 11, 5723-5736 (2015).
     [ local PDF: JCTC link ]

JC Robertson and TE Cheatham, III. "DNA backbone BI/BII distribution and dynamics in E2 protein-bound environment determined by molecular dynamics simulation." J. Phys. Chem. B 119, 14111-14119 (2015).
     [ local PDF: JPC B link ]

R Galindo-Murillo and TE Cheatham, III. "Using information about DNA structure and dynamics from experiment and simulation to give insight into genome-wide association studies." Chapter 4 in Translation Cardiometabolic Genomic Medicine, edited by A Rodriguez-Oquendo, p 81-98 (2015).

JC Thibault, DR Roe, K Eilbeck, TE Cheatham, III, and JC Facelli. "Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models, and ontology." SAR and QSAR in Environmental Research DOI: 10.1080/1062936X.2015.1076515 (2015).

C Bergonzo, KB Hall, and TE Cheatham, III. "Stem-loop V of Varkud satellite RNA exhibits characteristics of the Mg2+ bound structure in the presence of monovalent ions." J. Phys. Chem. B 119, 12355-12364 (2015).
     [ local PDF: JPC B link ]

C Bergonzo and TE Cheatham, III "Improved force field parameters lead to a better description of RNA structure" J. Chem. Theory Comp. 11, 3969-3972 [doi:10.1261/acs.jctc.5b00444] (2015).
     [ local PDF: JPC B link ]

AC Simmonett, FC Pickard IV, Y Shao, TE Cheatham, III and BR Brooks "Efficient treatment of induced diploles". J. Chem. Phys. 143, 074115 (2015).

C Bergonzo, NM Henriksen, DR Roe, and TE Cheatham, III "Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields." RNA 29: 1578-1590 [doi:10.1261/rna.051102.115] (2015).
     [ local PDF: RNA link ]

R Galindo-Murillo, JC Garcia-Ramos, L Ruiz-Azuara, TE Cheatham, III, and F Cortes-Guzman. "Intercalation processes of copper complexes in DNA." Nuc. Acids Res. 43: 5364-5376 (2015).
     [ local PDF: NAR link ]

TE Cheatham, III and DR Roe. "The impact of heterogeneous computing on workflows for biomolecular simulation and analysis." Computing in Science and Engineering 17:2, 30-39 (2015).
     [ local PDF: CiSE link ]

R Galindo-Murillo, DR Roe, and TE Cheatham, III. "Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)." Biochimica Biophys. Acta 1850, 1041-1058 (2015). doi: 10.1016/j.bbagen.2014.09.007.
     [ local PDF: BBAGEN link ]


2014

M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, TE Cheatham, III, PD Dans, B Jayaram, F Lankas, C Laughton, J Mitchell, R Osman, M Orozco, A Perez, D Petkeviciute, N Spackova, J Sponer, K Zakrzewska, and R Lavery. "μABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA." Nuc. Acids Res. 42, 12272-12283 (2014).
     [ local PDF: NAR link ]

R Galindo-Murillo, DR Roe, and TE Cheatham, III. "On the absence of intrahelical DNA dynamics on the μs to ms timescale." Nature Commun. 5:5152 (2014) doi: 10.1038/ncomms6152.
     [ local PDF: Nature Commun. link ]

Z Lin, M Koch, M Abdel Aziz, D Tianero, R Galindo, TE Cheatham, III, L Barrows, C Reilly, and E Schmidt. "Oxazinin A, A Pseudodimeric Natural Product of Mixed Bio-synthetic Origin from a Filamentous Fungus." Organic Letters 16, 4774-4777 (2014) doi: 10.1021/ol502227x.
     [ local PDF: Organic Letters link ]

P Stadlbauer, L Trantírek, TE Cheatham, J Koèa and J Sponer. "Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations." Biochimie 105, 22-35 (2014) doi:10.1016/j.biochi.2014.07.009.
     [ local PDF: Biochemie link ]

A Okal, S Cornillie, SJ Matissek, KJ Matissek, TE Cheatham, III and CS Lim. "A re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity." Mol. Pharm. 11(7), 2442-2452 (2014).
     [ local PDF: Mol. Pharm. link ]

NM Henriksen, H Hayatshahi, DR Davis, and TE Cheatham, III. "Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations." J. Chem. Info Model. 54(6), 1758-1772 (2014).
     [ local PDF: JCIM link ]

J Thibault, TE Cheatham, III, and JC Facelli. "iBIOMES Lite: Summarizing biomolecular simulation data in limited settings." J. Chem. Info Model. 54(6), 1810-1819 (2014).
     [ local PDF: JCIM link ]

R Galindo-Murillo and T.E. Cheatham, III. "DNA-binding dynamics and energetics of Co, Ni, and Cu metallopeptides" Chem. Med. Chem. 9(6), 1252-1259 (2014).
     [ local PDF: ChemMedChem link ]

DR Roe, C Bergonzo, and T.E. Cheatham, III. "Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods." J. Phys. Chem. B 118, 3543-3552 (2014).
     [ local PDF: JPCB link ]

JC Thibault, DR Roe, JC Facelii and T.E. Cheatham, III. "Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing." J. Cheminformatics 6 (2014) doi:10.1186/1758-2946-6-4.
     [ local PDF: J. Cheminformatics link ]

R Galindo-Murillo, C Bergonzo and T.E. Cheatham, III. "Molecular modeling of nucleic acid structure: Setup and analysis." Cur. Protocols Nucleic Acid Chemistry 56: 7.10.1-7.10.12 (2014).
     [ local PDF: CPNC link ]

C Bergonzo, N Henriksen, D Roe, J Swails, AE Roitberg, and T.E. Cheatham, III. "Multi-dimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide." J. Chem. Theory Comp. 10, 492-499 (2014).
     [ local PDF: JCTC link ]


2013

N Ashton, DR Roe, R Weiss, TE Cheatham III and R. Stewart. "Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis." Biomacromolecules 14, 3668-3681 (2013).
     [ local PDF: ACS link ]

R Galindo-Murillo, C Bergonzo and TE Cheatham, III. "Molecular modeling of nucleic acid structure." Current Protocols Nucleic Acid Chemistry 54: 7.5.1-7.5.13 (2013).
     [ local PDF: CPNC link ]

C Bergonzo, R Galindo-Murillo, and TE Cheatham, III. "Molecular modeling of nucleic acid structure: Energy and Sampling." Current Protocols Nucleic Acid Chemistry 54: 7.8.1-7.8.21 (2013).
     [ local PDF: CPNC link ]

C Bergonzo, R Galindo-Murillo and TE Cheatham, III. "Molecular modeling of nucleic acid structure: Electrostatics and solvation" Current Protocols Nucleic Acid Chemistry 55: 7.9.1-7.9.27 (2013).
     [ local PDF: CPNC link ]

TE Cheatham, III and D.A. Case. "Twenty-five years of nucleic acid simulations."Biopolymers [in press] (2013).
     [ local PDF: Biopolymers link ]

D Roe and TE Cheatham, III. "PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data." J. Chem. Theory Comp. 9, 3084-3095(2013). ...the long awaited PTRAJ paper!
     [ local PDF: JCTC link ]

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. 135, 9785-9796 (2013).
     [ local PDF: JACS link ]

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. 41, 7128-7143 (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 117m 491404927 (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. 53, 726-736 (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).
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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)
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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 ]