Thomas E Cheatham

发表

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.

Jianyin Shao, Stephen W Tanner, Nephi Thompson, 2007, Journal of chemical theory and computation.

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

Daniel R Roe, Thomas E Cheatham, T. Cheatham, 2013, Journal of chemical theory and computation.

Efficient treatment of induced dipoles.

Andrew C Simmonett, Bernard R Brooks, Yihan Shao, 2015, The Journal of chemical physics.

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution.

Pavel Hobza, Filip Lankas, Luc Van Meervelt, 2003, Journal of the American Chemical Society.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Daniel Svozil, Charles A Laughton, Modesto Orozco, 2007, Biophysical journal.

An accurate and simple quantum model for liquid water.

Wei Zhang, Gregory A Voth, Francesco Paesani, 2006, The Journal of chemical physics.

Twenty-five years of nucleic acid simulations.

David A Case, Thomas E Cheatham, D. Case, 2013, Biopolymers.

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.

Daniel Svozil, F. J. Luque, Modesto Orozco, 2008, The journal of physical chemistry. B.

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.

Jaroslav Koca, Thomas E Cheatham, J. Šponer, 2004, Biophysical journal.

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Niel M. Henriksen, Daniel R Roe, Thomas E Cheatham, 2015, RNA.

Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer.

Ly Le, Jack A Tuszynski, Thanh N Truong, 2010, The journal of physical chemistry. B.

Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.

Stefan Grimme, Arnošt Mládek, Jiří Šponer, 2013, Journal of the American Chemical Society.

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.

Jaroslav Koca, Thomas E Cheatham, J. Šponer, 2003, Biophysical journal.

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

Niel M. Henriksen, Daniel R Roe, Thomas E Cheatham, 2013, The journal of physical chemistry. B.

Simulation and modeling of nucleic acid structure, dynamics and interactions.

Thomas E Cheatham, T. Cheatham, 2004, Current opinion in structural biology.

Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis.

Russell J Stewart, Daniel R Roe, Thomas E Cheatham, 2013, Biomacromolecules.

Improved Force Field Parameters Lead to a Better Description of RNA Structure.

Thomas E Cheatham, Christina Bergonzo, T. Cheatham, 2015, Journal of chemical theory and computation.

DNA basepair step deformability inferred from molecular dynamics simulations.

Jörg Langowski, Filip Lankas, Thomas E Cheatham, 2003, Biophysical journal.

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.

Heinz Sklenar, Roman Osman, Richard Lavery, 2005, Biophysical journal.

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.

Heinz Sklenar, Roman Osman, Richard Lavery, 2004, Biophysical journal.

The ABCs of molecular dynamics simulations on B-DNA, circa 2012

Mihaly Mezei, Thomas E Cheatham, M. Mezei, 2012, Journal of Biosciences.

Structure-Activity Relationship of Capsaicin Analogs and Transient Receptor Potential Vanilloid 1-Mediated Human Lung Epithelial Cell Toxicity

Thomas E Cheatham, Manivannan Ethirajan, Kiumars Shahrokh, 2011, Journal of Pharmacology and Experimental Therapeutics.