Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide

por Winkler, Lauren, Cheatham, Thomas E.
Publicado 2023

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

por Joung, In Suk, Cheatham,, Thomas E.
Publicado 2008

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

por Joung, In Suk, Cheatham, Thomas E.
Publicado 2009

Mg(2+) Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction

por Bergonzo, Christina, Cheatham, Thomas E.
Publicado 2017

Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations

por Galindo-Murillo, Rodrigo, Cheatham, Thomas E
Publicado 2021

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

por Cang, Xiaohui, Šponer, Jiří, Cheatham, Thomas E.
Publicado 2011

Structures and Dynamics of DNA Mini-Dumbbells Are Force Field Dependent

por Winkler, Lauren, Galindo-Murillo, Rodrigo, Cheatham, Thomas E.
Publicado 2023

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

por Roe, Daniel R., Bergonzo, Christina, Cheatham, Thomas E.
Publicado 2014

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

por Bergonzo, Christina, Hall, Kathleen B., Cheatham, Thomas E.
Publicado 2015

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

por Bergonzo, Christina, Hall, Kathleen B., Cheatham, Thomas E.
Publicado 2016

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

por Thibault, Julien C., Cheatham, Thomas E., Facelli, Julio C.
Publicado 2014

On the absence of intra-helical DNA dynamics on the µs to ms timescale

por Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.
Publicado 2014

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...

por Joung, In Suk, Persil Çetinkol, Özgül, Hud, Nicholas V., Cheatham, Thomas E.
Publicado 2009

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

por Stadlbauer, Petr, Krepl, Miroslav, Cheatham, Thomas E., Koča, Jaroslav, Šponer, Jiří
Publicado 2013

Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations

por Henriksen, Niel M., Hayatshahi, Hamed S., Davis, Darrell R., Cheatham, Thomas E.
Publicado 2014

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

por Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Cheatham, Thomas E.
Publicado 2015

Computational Modeling of Stapled Coiled-Coil Inhibitors Against Bcr-Abl: Toward a Treatment Strategy for CML

por Lima, Maria Carolina P., Hornsby, Braxten D., Lim, Carol S., Cheatham, Thomas E.
Publicado 2023

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

por Thibault, Julien C, Roe, Daniel R, Facelli, Julio C, Cheatham, Thomas E
Publicado 2014

Assessing the Current State of Amber Force Field Modifications for DNA—2023 Edition

por Love, Olivia, Galindo-Murillo, Rodrigo, Zgarbová, Marie, Šponer, Jiří, Jurečka, Petr, Cheatham, Thomas E.
Publicado 2023

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

por Hayatshahi, Hamed S., Roe, Daniel R., Galindo-Murillo, Rodrigo, Hall, Kathleen B., Cheatham, Thomas E.
Publicado 2016