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High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants

Biomolecules (Basel, Switzerland), 2022-07, Vol.12 (7), p.940

2022

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Ion Motions in Molecular Dynamics Simulations on DNA

Proceedings of the National Academy of Sciences - PNAS, 2004-10, Vol.101 (41), p.14771-14775

2004

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A Statistical Thermodynamic Model for Investigating the Stability of DNA Sequences from Oligonucleotides to Genomes

Biophysical journal, 2014-06, Vol.106 (11), p.2465-2473

2014

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Estradiol induces allosteric coupling and partitioning of sex-hormone-binding globulin monomers among conformational states

iScience, 2021-06, Vol.24 (6), p.102414-102414, Article 102414

2021

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Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

The journal of physical chemistry. B, 2017-06, Vol.121 (22), p.5509-5514

2017

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Molecular dynamics of mismatch detection—How MutS uses indirect readout to find errors in DNA

Biophysical journal, 2023-08, Vol.122 (15), p.3031-3043

2023

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Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis

The journal of physical chemistry. B, 2023-01, Vol.127 (3), p.623-633

2023

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Spectral analysis of molecular dynamics simulations on PDZ: MD sectors

Journal of biomolecular structure & dynamics, 2020-02, Vol.38 (3), p.781-790

2020

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Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein

The journal of physical chemistry. B, 2017-03, Vol.121 (9), p.2049-2061

2017

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Toward a Universal Structural and Energetic Model for Prokaryotic Promoters

Biophysical journal, 2018-10, Vol.115 (7), p.1180-1189

2018

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Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

Journal of the American Chemical Society, 2009-02, Vol.131 (5), p.1724-1735

2009

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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

Biophysical journal, 2005-12, Vol.89 (6), p.3721-3740

2005

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

Journal of biosciences, 2012-07, Vol.37 (3), p.379-397

2012

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56 Molecular dynamics simulation studies of protein sectors: motional correlations

Journal of biomolecular structure & dynamics, 2015-05, Vol.33 (sup1), p.38-38

2015

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Nucleic acids: theory and computer simulation, Y2K

Current Opinion in Structural Biology, 2000-04, Vol.10 (2), p.182-196

2000

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Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Journal of biosciences, 2012-07, Vol.37 (3), p.399-421

2012

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Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A−RNA Complex

Journal of the American Chemical Society, 2006-07, Vol.128 (28), p.8992-8993

2006

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Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model

Journal of molecular biology, 2007-08, Vol.371 (5), p.1405-1419

2007

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A study of collective atomic fluctuations and cooperativity in the U1A–RNA complex based on molecular dynamics simulations

Journal of structural biology, 2007-03, Vol.157 (3), p.500-513

2007

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Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations

Biophysical journal, 2008-06, Vol.94 (11), p.4173-4183

2008

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U1A protein-stem loop 2 RNA recognition: Prediction of structural differences from protein mutations

Biopolymers, 2011-09, Vol.95 (9), p.591-606

2011

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Identification of an Aminoacridine Derivative That Binds to RNA Tetraloops

Journal of medicinal chemistry, 2007-08, Vol.50 (17), p.4096-4104

2007

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Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Bioinformatics, 2006-04, Vol.22 (8), p.1007-1009

2006

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Characterization of the Dynamics of an Essential Helix in the U1A Protein by Time-Resolved Fluorescence Measurements

The journal of physical chemistry. B, 2008-05, Vol.112 (19), p.6122-6130

2008

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Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

Journal of chemical information and modeling, 2006-05, Vol.46 (3), p.1084-1093

2006

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High Energy Channeling and Malleable Transition States: Molecular Dynamics Simulations and Free Energy Landscapes for the Thermal Unfolding of Protein U1A and 13 Mutants

Ion Motions in Molecular Dynamics Simulations on DNA

A Statistical Thermodynamic Model for Investigating the Stability of DNA Sequences from Oligonucleotides to Genomes

Estradiol induces allosteric coupling and partitioning of sex-hormone-binding globulin monomers among conformational states

Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

Molecular dynamics of mismatch detection—How MutS uses indirect readout to find errors in DNA

Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis

Spectral analysis of molecular dynamics simulations on PDZ: MD sectors

Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein

Toward a Universal Structural and Energetic Model for Prokaryotic Promoters

Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

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

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

56 Molecular dynamics simulation studies of protein sectors: motional correlations

Nucleic acids: theory and computer simulation, Y2K

Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A−RNA Complex

Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model

A study of collective atomic fluctuations and cooperativity in the U1A–RNA complex based on molecular dynamics simulations

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations

U1A protein-stem loop 2 RNA recognition: Prediction of structural differences from protein mutations

Identification of an Aminoacridine Derivative That Binds to RNA Tetraloops

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Characterization of the Dynamics of an Essential Helix in the U1A Protein by Time-Resolved Fluorescence Measurements

Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

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