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

by Cang, Xiaohui, Šponer, Jiří, Cheatham, Thomas E.
Published 2011

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

by Roe, Daniel R., Bergonzo, Christina, Cheatham, Thomas E.
Published 2014

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

by Thibault, Julien C., Cheatham, Thomas E., Facelli, Julio C.
Published 2014

Stem-Loop V of Varkud Satellite RNA Exhibits Characteristics of the Mg2+ Bound Structure in the Presence of Monovalent Ions

by Bergonzo, Christina, Hall, Kathleen B., Cheatham, Thomas E.
Published 2015

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

by Galindo-Murillo, Rodrigo, Roe, Daniel R., Cheatham, Thomas E.
Published 2014

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

by Bergonzo, Christina, Hall, Kathleen B., Cheatham, Thomas E.
Published 2016

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

by Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Mládek, Arnošt, Banáš, Pavel, Cheatham, Thomas E., Jurečka, Petr
Published 2011

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

by Stadlbauer, Petr, Krepl, Miroslav, Cheatham, Thomas E., Koča, Jaroslav, Šponer, Jiří
Published 2013

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

by Henriksen, Niel M., Hayatshahi, Hamed S., Davis, Darrell R., Cheatham, Thomas E.
Published 2014

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

by Thibault, Julien C, Roe, Daniel R, Facelli, Julio C, Cheatham, Thomas E
Published 2014

Intercalation processes of copper complexes in DNA

by Galindo-Murillo, Rodrigo, García-Ramos, Juan Carlos, Ruiz-Azuara, Lena, Cheatham, Thomas E., Cortés-Guzmán, Fernando
Published 2015

Re-Engineered p53 Chimera with Enhanced Homo-Oligomerization That Maintains Tumor Suppressor Activity

by Okal, Abood, Cornillie, Sean, Matissek, Stephan J., Matissek, Karina J., Cheatham, Thomas E., Lim, Carol S.
Published 2014

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

by Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Swails, Jason M., Roitberg, Adrian E., Cheatham, Thomas E.
Published 2013

Assessing the Current State of Amber Force Field Modifications for DNA

by Galindo-Murillo, Rodrigo, Robertson, James C., Zgarbová, Marie, Šponer, Jiří, Otyepka, Michal, Jurečka, Petr, Cheatham, Thomas E.
Published 2016

Oxazinin A, a Pseudodimeric Natural Product of Mixed Biosynthetic Origin from a Filamentous Fungus

by Lin, Zhenjian, Koch, Michael, Abdel Aziz, May Hamdy, Galindo-Murillo, Rodrigo, Tianero, Ma. Diarey, Cheatham, Thomas E., Barrows, Louis R., Reilly, Chris A., Schmidt, Eric W.
Published 2014