Publications by authors named "David D L Minh"

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Molecular Dynamics Analysis of Inhibitor Binding Interactions in the Vibrio cholerae Respiratory Complex NQR.
Joseph A DePaolo-Boisvert, Karina Tuz, David D L Minh, Oscar X Juarez

Proteins· September 2025

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Enzyme kinetics model for the coronavirus main protease including dimerization and ligand binding.
Van N T La, Lulu Kang, David D L Minh

Biophys J· August 2025

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Intracellular Pocket Conformations Determine Signaling Efficacy through the μ Opioid Receptor.
David A Cooper, Joseph DePaolo-Boisvert, Stanley A Nicholson, Barien Gad, David D L Minh

J Chem Inf Model· February 2025

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Enzyme kinetics model for the coronavirus main protease including dimerization and ligand binding.
Van Ngoc Thuy La, Lulu Kang, David D L Minh

bioRxiv· January 2025

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Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid Receptor.
David D L Minh, David A Cooper, Bing Xie, Lei Shi

J Chem Theory Comput· January 2025

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Intracellular pocket conformations determine signaling efficacy through the opioid receptor.
David A Cooper, Joseph DePaolo-Boisvert, Stanley A Nicholson, Barien Gad, David D L Minh

bioRxiv· December 2024

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On Inactivation of the Coronavirus Main Protease.
Hong Ha Nguyen, Jim Tufts, David D L Minh

J Chem Inf Model· March 2024

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Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation.
Van N T La, David D L Minh

Int J Mol Sci· October 2023

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Inclusion of Control Data in Fits to Concentration-Response Curves Improves Estimates of Half-Maximal Concentrations.
Van Ngoc Thuy La, Stanley Nicholson, Amna Haneef, Lulu Kang, David D L Minh

J Med Chem· September 2023

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Learned mappings for targeted free energy perturbation between peptide conformations.
Soohaeng Yoo Willow, Lulu Kang, David D L Minh

J Chem Phys· September 2023

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H-Bonds in Crambin: Coherence in an α-Helix.
Stanley Nicholson, David D L Minh, Robert Eisenberg

ACS Omega· April 2023

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Bayesian regression and model selection for isothermal titration calorimetry with enantiomeric mixtures.
Trung Hai Nguyen, Van N T La, Kyle Burke, David D L Minh

PLoS One· October 2022

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Identification of the riboflavin cofactor-binding site in the Vibrio cholerae ion-pumping NQR complex: A novel structural motif in redox enzymes.
Karina Tuz, Ming Yuan, Yuyao Hu, Tien T T Do, Soohaeng Yoo Willow, David D L Minh

J Biol Chem· August 2022

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Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR.
Soohaeng Yoo Willow, Ming Yuan, Oscar Juárez, David D L Minh

Proteins· October 2021

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Implicit ligand theory for relative binding free energies: II. An estimator based on control variates.
Trung Hai Nguyen, David D L Minh

J Phys Commun· November 2020

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Robosample: A rigid-body molecular simulation program based on robot mechanics.
Laurentiu Spiridon, Teodor Asvadur Şulea, David D L Minh, Andrei-Jose Petrescu

Biochim Biophys Acta Gen Subj· August 2020

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A Structural Model for Bax∆2-Mediated Activation of Caspase 8-Dependent Apoptosis.
Bing Xie, Qi Yao, Jialing Xiang, David D L Minh

Int J Mol Sci· July 2020

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On the polarization of ligands by proteins.
Soohaeng Yoo Willow, Bing Xie, Jason Lawrence, Robert S Eisenberg, David D L Minh

Phys Chem Chem Phys· June 2020

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Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.
David D L Minh

J Comput Chem· March 2020

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On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.
William M Menzer, Bing Xie, David D L Minh

J Comput Chem· March 2020

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Nonequilibrium path-ensemble averages for symmetric protocols.
Trung Hai Nguyen, Van Ngo, João Paulo Castro Zerba, Sergei Noskov, David D L Minh

J Chem Phys· November 2019

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Role of Subunit D in Ubiquinone-Binding Site of NQR: Pocket Flexibility and Inhibitor Resistance.
Daniel A Raba, Ming Yuan, Xuan Fang, William M Menzer, Bing Xie, David D L Minh

ACS Omega· November 2019

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Conserved residue His-257 of flavin transferase ApbE plays a critical role in substrate binding and catalysis.
Xuan Fang, Jerzy Osipiuk, Srinivas Chakravarthy, Ming Yuan, William M Menzer, David D L Minh

J Biol Chem· September 2019

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Correction to "Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles".
Bing Xie, John D Clark, David D L Minh

J Chem Inf Model· February 2019

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Design, Synthesis, and Biological Evaluation of Polyaminocarboxylate Ligand-Based Theranostic Conjugates for Antibody-Targeted Cancer Therapy and Near-Infrared Optical Imaging.
Siyuan Ren, Xiang Sun, Haixing Wang, Trung Hai Nguyen, Negar Sadeghipour, David D L Minh

ChemMedChem· December 2018

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