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Theoretical and Computational Chemistry

Working Paper

Expanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Si Zhang, David Hahn, Michael R. Shirts, Vincent Voelz

Version 1 posted 26 May 2021

432

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Theoretical and Computational Chemistry

Working Paper

Testing for Physical Validity in Molecular Simulations

Pascal T. Merz, Michael R. Shirts

Version 2 posted 24 July 2018

952

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Theoretical and Computational Chemistry

Working Paper

Toward Learned Chemical Perception of Force Field Typing Rules

Camila Zanette, Caitlin C. Bannan, Christopher I. Bayly, Josh Fass, Michael Gilson, Michael R. Shirts, John Chodera, David Mobley

Version 3 posted 15 October 2018

1,313

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Theoretical and Computational Chemistry

Working Paper

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Christopher Walker, Garrett Meek, Theodore Fobe, Michael R. Shirts

Version 1 posted 28 May 2021

233

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Theoretical and Computational Chemistry

Working Paper

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

Yudong Qiu, Daniel Smith, Simon Boothroyd, Hyesu Jang, Jeffrey Wagner, Caitlin C. Bannan, Trevor Gokey, Victoria T. Lim, Chaya Stern, Andrea Rizzi, Xavier Lucas, Bryon Tjanaka, Michael R. Shirts, Michael Gilson, John Chodera, Christopher I. Bayly, David Mobley, Lee-Ping Wang

Version 4 posted 09 August 2021

1,941

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation

Wei-Tse Hsu, Dominique Ramirez, Tarek Sammakia, Zhongping Tan, Michael Shirts

Version 3 posted 02 March 2022

515

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Theoretical and Computational Chemistry

Working Paper

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

Simon Boothroyd, Lee-Ping Wang, David Mobley, John Chodera, Michael Shirts

Version 1 posted 05 August 2021

744

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1

Citations

Theoretical and Computational Chemistry

Working Paper

Improving force field accuracy by training against condensed phase mixture properties

Simon Boothroyd, Owen Madin, David Mobley, Lee-Ping Wang, John Chodera, Michael Shirts

Version 3 posted 15 April 2022

775

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Theoretical and Computational Chemistry

Working Paper

Obtaining and characterizing stable bicontinuous cubic morphologies and their nanochannels in lyotropic liquid crystal membranes

Subin Sahu, Nathanael Schwindt, Benjamin Coscia, Michael Shirts

Version 1 posted 02 September 2022

297

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Theoretical and Computational Chemistry

Working Paper

Assessing the accuracy and efficiency of free energy differences obtained from reweighted flow-based probabilistic generative models

Edgar Olehnovics, Yifei Michelle Liu, Nada Mehio, Ahmad Y Sheikh, Michael Shirts, Matteo Salvalaglio

Version 3 posted 25 June 2024

461

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16 results in Michael Shirts in Authors: Michael Shirts

Expanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies

Testing for Physical Validity in Molecular Simulations

Toward Learned Chemical Perception of Force Field Typing Rules

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation

The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

Improving force field accuracy by training against condensed phase mixture properties

Obtaining and characterizing stable bicontinuous cubic morphologies and their nanochannels in lyotropic liquid crystal membranes

Assessing the accuracy and efficiency of free energy differences obtained from reweighted flow-based probabilistic generative models

16 results in Authors: Michael Shirts