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Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations

Biophysical journal, 2005-04, Vol.88 (4), p.2472-2493

2005

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The Extent of Pyrene Excimer Fluorescence Emission Is a Reflector of Distance and Flexibility: Analysis of the Segment Linking the LDL Receptor-Binding and Tetramerization Domains of Apolipoprotein E3

Biochemistry (Easton), 2012-08, Vol.51 (31), p.6207-6219

2012

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A Comprehensive Review of Cholinesterase Modeling and Simulation

Biomolecules (Basel, Switzerland), 2021-04, Vol.11 (4), p.580

2021

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A Hands-On Collaboration-Ready Single- or Interdisciplinary Computational Exercise in Molecular Recognition and Drug Design

Education sciences, 2024-01, Vol.14 (2), p.139

2024

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Direct calculation of the binding free energies of FKBP ligands

The Journal of chemical physics, 2005-08, Vol.123 (8), p.084108-084108-5

2005

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Simulations of the Role of Water in the Protein-Folding Mechanism

Proceedings of the National Academy of Sciences - PNAS, 2004-04, Vol.101 (17), p.6456-6461

2004

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Evaluating molecular mechanical potentials for helical peptides and proteins

PloS one, 2010-04, Vol.5 (4), p.e10056

2010

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Unusual Compactness of a Polyproline Type II Structure

Proceedings of the National Academy of Sciences - PNAS, 2005-08, Vol.102 (33), p.11698-11703

2005

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Biopolymers, 2003-01, Vol.68 (1), p.91-109

2003

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Does Water Play a Structural Role in the Folding of Small Nucleic Acids?

Biophysical journal, 2005-04, Vol.88 (4), p.2516-2524

2005

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Overcoming the Heuristic Nature of k -Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes

Journal of chemical information and modeling, 2020-06, Vol.60 (6), p.3081-3092

2020

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Energetically unfavorable protein angles: Exploration of a conserved dihedral angle in triosephosphate isomerase

Biopolymers, 2022-11, Vol.113 (11), p.e23525-n/a

2022

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Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

Nucleic acids research, 2010-08, Vol.38 (14), p.4856

2010

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Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcholinesterase inhibitors

Bioorganic & medicinal chemistry, 2017-06, Vol.25 (12), p.3171-3181

2017

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Nanotube Confinement Denatures Protein Helices

Journal of the American Chemical Society, 2006-05, Vol.128 (19), p.6316-6317

2006

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Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot

Nucleic acids research, 2017-05, Vol.45 (8), p.4893

2017

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Understanding the enzyme-ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition

Journal of biomolecular structure & dynamics, 2020-03, Vol.38 (4), p.1028-1041

2020

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Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories

Journal of computational chemistry, 2008-08, Vol.29 (11), p.1740-1752

2008

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Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

Journal of computational chemistry, 2005-05, Vol.26 (7), p.682-690

2005

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Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations

Biophysical journal, 2003-08, Vol.85 (2), p.790-803

2003

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RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

Journal of molecular biology, 2002-04, Vol.317 (4), p.493-506

2002

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The Solvation Interface is a Determining Factor in Peptide Conformational Preferences

Journal of molecular biology, 2006-02, Vol.356 (1), p.248-256

2006

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Ensemble Simulations: Folding, Unfolding and Misfolding of High-Efficiency Transfer-Messenger RNA Pseudoknot

Biophysical journal, 2021-02, Vol.120 (3), p.314a-314a

2021

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Does Native State Topology Determine the RNA Folding Mechanism?

Journal of molecular biology, 2004-04, Vol.337 (4), p.789-797

2004

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How well can simulation predict protein folding kinetics and thermodynamics?

Annual review of biophysics and biomolecular structure, 2005-01, Vol.34 (1), p.43-69

2005

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Exploring the Helix-Coil Transition via All-Atom Equilibrium Ensemble Simulations

The Extent of Pyrene Excimer Fluorescence Emission Is a Reflector of Distance and Flexibility: Analysis of the Segment Linking the LDL Receptor-Binding and Tetramerization Domains of Apolipoprotein E3

A Comprehensive Review of Cholinesterase Modeling and Simulation

A Hands-On Collaboration-Ready Single- or Interdisciplinary Computational Exercise in Molecular Recognition and Drug Design

Direct calculation of the binding free energies of FKBP ligands

Simulations of the Role of Water in the Protein-Folding Mechanism

Evaluating molecular mechanical potentials for helical peptides and proteins

Unusual Compactness of a Polyproline Type II Structure

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Does Water Play a Structural Role in the Folding of Small Nucleic Acids?

Overcoming the Heuristic Nature of k -Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes

Energetically unfavorable protein angles: Exploration of a conserved dihedral angle in triosephosphate isomerase

Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcholinesterase inhibitors

Nanotube Confinement Denatures Protein Helices

Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot

Understanding the enzyme-ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition

Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories

Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

Insights into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations

RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

The Solvation Interface is a Determining Factor in Peptide Conformational Preferences

Ensemble Simulations: Folding, Unfolding and Misfolding of High-Efficiency Transfer-Messenger RNA Pseudoknot

Does Native State Topology Determine the RNA Folding Mechanism?

How well can simulation predict protein folding kinetics and thermodynamics?

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