List of works - Thomas E. Cheatham, III

A coarse-grained model of DNA with explicit solvation by water and ions

scientific article

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

scientific article

Advancing the Workforce That Supports Computationally and Data Intensive Research

scientific article published on 21 July 2021

Ancillary Ligand in Ternary Cu<sup>II</sup> Complexes Guides Binding Selectivity toward Minor-Groove DNA

scientific article published on 15 December 2020

Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins

scientific article

Araiosamines A-D: tris-bromoindole cyclic guanidine alkaloids from the marine sponge Clathria (Thalysias) araiosa

scientific article

Assessing the Current State of Amber Force Field Modifications for DNA

scientific article

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

scientific article published in November 2007

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

scientific article published on 16 December 2016

Computational DNA binding studies of (-)-epigallocatechin-3-gallate

scientific article

Computational Modeling of Stapled Peptides toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics.

scientific article published on 8 March 2018

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing

scientific article published on May 2006

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

scientific article

Consensus conformations of dinucleotide monophosphates described with well-converged molecular dynamics simulations.

scientific article

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

scientific article

Correction to "improved coiled-coil design enhances interaction with bcr-abl and induces apoptosis".

scientific article

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

scientific article

DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations

scientific article published on 19 October 2015

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations ⬇️

scientific article published on November 1, 2003

DNA deformability at the base pair level.

scientific article

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

scientific article

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

scientific article published on 2 July 2008

Disruption of Bcr-Abl coiled coil oligomerization by design

scientific article

Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

scientific article published on 13 June 2016

Efficient treatment of induced dipoles

scientific article published in August 2015

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods

scientific article

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

scientific article

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

scientific article published on February 2010

Exploring potentially alternative non-canonical DNA duplex structures through simulation

scientific article published on 17 November 2018

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

scientific article

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

scientific article

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

scientific article

Improved Cytochrome P450 3A4 Molecular Models Accurately Predict the Phe215 Requirement for Raloxifene Dehydrogenation Selectivity ⬇️

scientific article published on October 19, 2010

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

scientific article

Improved coiled-coil design enhances interaction with Bcr-Abl and induces apoptosis

scientific article published on 12 December 2011

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.

scientific article published on 06 January 2017

Inhibitor-induced structural change in the HCV IRES domain IIa RNA

scientific article

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis

scientific article published on 19 August 2011

Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA.

scientific article published on 13 April 2017

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

scientific article

Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.

scientific article

Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

scientific article

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

scientific article published on December 2009

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

scientific article

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

scientific article

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

scientific article

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

scientific article

Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters

scientific article published on October 2009

Molecular modeling of nucleic Acid structure: electrostatics and solvation

scientific article

Molecular modeling of nucleic Acid structure: setup and analysis

scientific article

Molecular modeling of nucleic acid structure: energy and sampling

scientific article published on 08 October 2013

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

scientific article

On the absence of intrahelical DNA dynamics on the μs to ms timescale

scientific article

Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus

scientific article published on 4 September 2014

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

scientific article

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

scientific article published on 02 December 2015

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

scientific article

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

scientific article

Re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity

scientific article

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

scientific article

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

scientific article published on 02 August 2011

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

article by Marie Zgarbová et al published 20 November 2015 in Journal of Chemical Theory and Computation

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

scientific article published on 19 June 2013

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

scientific article

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

scientific article published on 3 October 2013

Simulation and modeling of nucleic acid structure, dynamics and interactions

scientific article published on June 2004

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

scientific article

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions

scientific article

Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations

scientific article

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

scientific article published on 21 May 2013

Structurally minimized mu-conotoxin analogues as sodium channel blockers: implications for designing conopeptide-based therapeutics

scientific article published on March 2009

Structure-activity relationship of capsaicin analogs and transient receptor potential vanilloid 1-mediated human lung epithelial cell toxicity

scientific article

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

scientific article

The Amber biomolecular simulation programs

scientific article (publication date: December 2005)

Totopotensamides, polyketide-cyclic peptide hybrids from a mollusk-associated bacterium Streptomyces sp. ⬇️

scientific article published on 22 March 2012

Transitions of Double-Stranded DNA Between the A- and B-Forms

scientific article published on 02 May 2016

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

article

Twenty-five years of nucleic acid simulations

scientific article published on December 2013

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

scientific article published on 10 June 2016

iBIOMES Lite: summarizing biomolecular simulation data in limited settings

scientific article

iBIOMES: managing and sharing biomolecular simulation data in a distributed environment

scientific article

List of works by Thomas E. Cheatham, III

A coarse-grained model of DNA with explicit solvation by water and ions

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Advancing the Workforce That Supports Computationally and Data Intensive Research

Ancillary Ligand in Ternary Cu<sup>II</sup> Complexes Guides Binding Selectivity toward Minor-Groove DNA

Antifreeze proteins at the ice/water interface: three calculated discriminating properties for orientation of type I proteins

Araiosamines A-D: tris-bromoindole cyclic guanidine alkaloids from the marine sponge Clathria (Thalysias) araiosa

Assessing the Current State of Amber Force Field Modifications for DNA

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

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

Computational DNA binding studies of (-)-epigallocatechin-3-gallate

Computational Modeling of Stapled Peptides toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics.

Computational Science and Engineering Online (CSE-Online): a cyber-infrastructure for scientific computing

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

Consensus conformations of dinucleotide monophosphates described with well-converged molecular dynamics simulations.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Correction to "improved coiled-coil design enhances interaction with bcr-abl and induces apoptosis".

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations ⬇️

DNA deformability at the base pair level.

Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

Disruption of Bcr-Abl coiled coil oligomerization by design

Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

Efficient treatment of induced dipoles

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

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

Exploring potentially alternative non-canonical DNA duplex structures through simulation

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

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

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

Improved Cytochrome P450 3A4 Molecular Models Accurately Predict the Phe215 Requirement for Raloxifene Dehydrogenation Selectivity ⬇️

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

Improved coiled-coil design enhances interaction with Bcr-Abl and induces apoptosis

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.

Inhibitor-induced structural change in the HCV IRES domain IIa RNA

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis

Investigating the ion dependence of the first unfolding step of GTPase-Associating Center ribosomal RNA.

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils.

Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

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

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

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

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

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

Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters

Molecular modeling of nucleic Acid structure: electrostatics and solvation

Molecular modeling of nucleic Acid structure: setup and analysis

Molecular modeling of nucleic acid structure: energy and sampling

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

On the absence of intrahelical DNA dynamics on the μs to ms timescale

Oxazinin A, a pseudodimeric natural product of mixed biosynthetic origin from a filamentous fungus

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

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

Re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

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

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

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

Simulation and modeling of nucleic acid structure, dynamics and interactions

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg(2+) Bound Structure in the Presence of Monovalent Ions

Structural and energetic analysis of 2-aminobenzimidazole inhibitors in complex with the hepatitis C virus IRES RNA using molecular dynamics simulations

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

Structurally minimized mu-conotoxin analogues as sodium channel blockers: implications for designing conopeptide-based therapeutics

Structure-activity relationship of capsaicin analogs and transient receptor potential vanilloid 1-mediated human lung epithelial cell toxicity

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

The Amber biomolecular simulation programs

Totopotensamides, polyketide-cyclic peptide hybrids from a mollusk-associated bacterium Streptomyces sp. ⬇️

Transitions of Double-Stranded DNA Between the A- and B-Forms

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

Twenty-five years of nucleic acid simulations