Thomas E. Cheatham, III

Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry, Director,
Center for High Peformance Computing, University of Utah

Office

SRB 4914
Phone: 801.587.9652

Fax: 801.585.6208

INSCC-410
Phone: 801.585.6318
Fax: 801.585.5366


Research Interests

Focus


The people in our lab use and develop molecular dynamics, free energy simulation, and trajectory analysis methodologies in applications aimed at better understanding biomolecular structure, dynamics and interactions. A strong focus of our funded efforts centers on the reliable representation of nucleic acid systems (DNA and RNA) in solution. For example, we helped solved the NMR structure of the drug-bound Hepatitis C virus IRES structure shown on the left. Based on this (and related structures), we can now apply CADD methods and simulation to better understand and design potential new Hepatitis C therapeutics. In addition, large efforts are underway to better characterize RNA structure and force fields through simulation of a large number of commonly observed RNA structural motifs and a large variety of NMR and crystal structures. We are also involved with international collaborative efforts to understand DNA structure, for example through the ABC consortium and long simulations of DNA...

Critical to reliable representation of the structure, dynamics and interactions is not only trying to simulation the biomolecules in their native solution environment but to also both critically assess and validate the simulation results with experiment. Our group focuses on both brute-force and enhanced sampling/ensemble-based simulation using available high performance computational resources at the University of Utah (www.chpc.utah.edu) and elsewhere. Outside resources include large allocations of computer time from Blue Waters, XSEDE (www.xsede.org), on the Anton machine at PSC and from other sources. With these resources we also are able to expose and overcome limitations in the methods and force fields...


Beyond nucleic acids, we are also interested in various coiled-coils, enzymes and cytochrome P450's. A key emphasis is on improving stability or understanding how ligands alter receptor structure upon binding. Also, in addition to continued development of the ptraj/cpptraj tools within the AmberTools suite for analysis of MD trajectories, we are exploring methods to mine more information from the simulation data and means to more broadly disseminate the MD results.

Although our primary development and simulation engine is AMBER, we also use and have experience with CHARMM, NAMD, and other programs.

Software

Follow the links to the software.


Grants

Research in the lab is currently funded by various research grants, including:

NIH RO1-GM081411: "Biomolecular simulation for the end-stage refinement of nucleic acid structure".
(2/01/08-1/31/14) PI: Cheatham.
This core R-01 funding supports research into the development of better force fields for simulation of RNA, attempts various means to assess and validate the performance of MD simulation as applied to RNA, and seeks to explore means to more broadly disseminate MD simulation data. Here is the NIH reporter link. Currently this is in no-cost-extension.

NIH RO1-GM098102: "RNA-ligand interactions: Simulation and experiment".
(9/30/11-8/31/15) M-PIs: Kathleen Hall (WUSTL), Cheatham and Carlos Simmerling (Stony Brook U).
This core R-01 funding supports research into the development of better force fields for simulation of RNA, attempts various means to assess and validate the performance of MD simulation as applied to RNA, and seeks to explore means to more broadly disseminate MD simulation data. Here is the NIH reporter link

NSF CHE-1266307: "CDS&E: Tools to facilitate deeper data analysis, exploration, management, and sharing of ensembles of molecular dynamics trajectory data".
(10/01/13-9/30/15) PI: Cheatham
Further development of the iBIOMES environment for sharing and disseminating MD simulation data and also tools for deeper analysis (CPPTRAJ).

NSF ACI-1341034: "CC-NIE Integration: Science slices converting network research innovation into enhanced capability for computational science and engineering at the University of Utah".
(10/01/13-9/30/15) PI: Corbato, Co-PIs: Bolton, van der Merwe, Ricci, Cheatham
Deployment of a science DMZ network at the U of Utah.

NSF OCI-1035208: "PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change".
(2/01/11-1/31/14) PI: Cheatham, Co-PIs: Simmerling (Stony Brook), Roitberg (U Florida), and York (Rutgers).
This is a travel grant that provides training and preparation for eventual usage of the "Blue Waters" supercomputer at NCSA. We are one of ~36 groups that will be given access. Here is the link to the NSF awards database..

NIH R01-GM074249: "P450-mediated dehydrogenation mechanisms."
(1/01/11-12/31/15) PI: Gs Yost    Co-PIs: Cheatham, Reilly
Experiment, simulation and docking probe the interaction of substrates with P450 with a focus on dehydrogenation reactions. Here is the NIH reporter link

NSF Cyberinfrastructure partnership, LRAC MCA01S027 (yearly)
"Insight into biomolecular structure, dynamics, interactions and energetics from simulation".
PI: Cheatham.
This is a large allocation of resources on the NSF supercomputer centers to support research in the Cheatham lab.

Recently ended grants

NIH R01-GM079383: "AMBER force field consortium: A coherent biomolecular simulation platform."
(9/28/07-8/31/12) PI: Y. Duan (UC Davis) Co-PIs: Cheatham, C. Simmerling (Stony Brook U), R. Luo (UC Irvine), P. Cieplak (Burnham Inst), and J. Wang.
The consortium aims to improve the AMBER force fields; our role focuses on polarizable force fields for nucleic acids. Here is the NIH reporter link.

Pittsburgh Supercomputing Center, PSCA00033P
"Molecular dynamics of DNA and protein-DNA complexes: A proposal for obtaining microsecond trajectories using Anton".
PI: Cheatham.

Pittsburgh Supercomputing Center, PSCA00067P
"Development and testing of improved fixed-charge force fields for proteins".
PI: Case.


Related Links

Cheatham's Laboratory Website

Visit Cheatham's Laboratory website


Publications

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. [in press] (2014).

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 ]

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 pii: S034-4165(14)00309-2 (2014). doi: 10.1016/j.bbagen.2014.09.007.
     [ local PDF: BBAGEN 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).
     [ 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 ]

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