Publications by authors named "RI Cukier"

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Machine learning can be used to distinguish protein families and generate new proteins belonging to those families.
Chi Jin, Robert I Cukier

J Chem Phys· November 2019

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Reweighting ensemble probabilities with experimental histogram data constraints using a maximum entropy principle.
Hongfeng Lou, Robert I Cukier

J Chem Phys· December 2018

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Hinge action versus grip in translocation by RNA polymerase.
Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier

Transcription· October 2018

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Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain.
Robert I Cukier

J Phys Chem B· October 2018

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Conformational Ensembles Exhibit Extensive Molecular Recognition Features.
Robert I Cukier

ACS Omega· August 2018

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Generating intrinsically disordered protein conformational ensembles from a Markov chain.
Robert I Cukier

J Chem Phys· March 2018

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Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA.
Chi Jin, David Cerutti, Robert I Cukier

J Phys Chem B· November 2017

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Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.
Rahul Banerjee, Honggao Yan, Robert I Cukier

J Phys Chem B· June 2015

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Dihedral angle entropy measures for intrinsically disordered proteins.
Robert I Cukier

J Phys Chem B· March 2015

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Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.
Beibei Wang, Kristopher Opron, Zachary F Burton, Robert I Cukier, Michael Feig

Nucleic Acids Res· January 2015

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Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation.
Jinxiang Liu, Robert I Cukier, Yuxiang Bu, Yuan Shang

J Chem Theory Comput· October 2014

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Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer.
Robert I Cukier

J Phys Chem B· September 2014

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Conformational transition of response regulator RR468 in a two-component system signal transduction process.
Rahul Banerjee, Honggao Yan, Robert I Cukier

J Phys Chem B· May 2014

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Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.
Rahul Banerjee, Robert I Cukier

J Phys Chem B· March 2014

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Computational simulation strategies for analysis of multisubunit RNA polymerases.
Beibei Wang, Michael Feig, Robert I Cukier, Zachary F Burton

Chem Rev· November 2013

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Variance of a potential of mean force obtained using the weighted histogram analysis method.
Robert I Cukier

J Phys Chem B· November 2013

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Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation.
Jinxiang Liu, Robert I Cukier, Yuxiang Bu

J Chem Theory Comput· November 2013

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Excess dielectron in an ionic liquid as a dynamic bipolaron.
Jinxiang Liu, Zhiping Wang, Meng Zhang, Robert I Cukier, Yuxiang Bu

Phys Rev Lett· March 2013

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The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.
Yuri A Nedialkov, Kristopher Opron, Fadi Assaf, Irina Artsimovitch, Maria L Kireeva, Robert I Cukier

Biochim Biophys Acta· February 2013

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Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.
Maria L Kireeva, Kristopher Opron, Steve A Seibold, Céline Domecq, Robert I Cukier

BMC Biophys· June 2012

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Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper.
Robert I Cukier

J Phys Chem B· May 2012

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Solvation and evolution dynamics of an excess electron in supercritical CO2.
Zhiping Wang, Jinxiang Liu, Meng Zhang, Robert I Cukier, Yuxiang Bu

Phys Rev Lett· May 2012

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Ferreting out correlations from trajectory data.
Robert I Cukier

J Chem Phys· December 2011

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A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.
Robert I Cukier

J Chem Phys· January 2011

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How many atoms are required to characterize accurately trajectory fluctuations of a protein?
Robert I Cukier

J Chem Phys· June 2010

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