Search Results - "Minh, David D. L."

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

“…We compare several different methods to quantify the uncertainty of binding parameters estimated from isothermal titration calorimetry data: the asymptotic…”
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Bayesian regression and model selection for isothermal titration calorimetry with enantiomeric mixtures by Nguyen, Trung Hai, La, Van N T, Burke, Kyle, Minh, David D L

“…Bayesian regression is performed to infer parameters of thermodynamic binding models from isothermal titration calorimetry measurements in which the titrant is…”
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Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation by Nilmeier, Jerome P, Crooks, Gavin E, Minh, David D. L, Chodera, John D

“…Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is…”
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Bayesian analysis of isothermal titration calorimetry for binding thermodynamics by Nguyen, Trung Hai, Rustenburg, Ariën S, Krimmer, Stefan G, Zhang, Hexi, Clark, John D, Novick, Paul A, Branson, Kim, Pande, Vijay S, Chodera, John D, Minh, David D L

“…Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment…”
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Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase by Onuk, Emre, Badger, John, Wang, Yu Jing, Bardhan, Jaydeep, Chishti, Yasmin, Akcakaya, Murat, Brooks, Dana H, Erdogmus, Deniz, Minh, David D. L, Makowski, Lee

“…Crystal structures of adenylate kinase (AdK) from Escherichia coli capture two states: an “open” conformation (apo) obtained in the absence of ligands and a…”
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The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics by Minh, David D. L, Chang, Chia-en, Trylska, Joanna, Tozzini, Valentina, McCammon, J. Andrew

“…High macromolecular concentrations, or crowded conditions, have been shown to affect a wide variety of molecular processes, including diffusion, association…”
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Role of Subunit D in Ubiquinone-Binding Site of Vibrio cholerae NQR: Pocket Flexibility and Inhibitor Resistance by Raba, Daniel A, Yuan, Ming, Fang, Xuan, Menzer, William M, Xie, Bing, Liang, Pingdong, Tuz, Karina, Minh, David D. L, Juárez, Oscar

“…The ion-pumping NADH: ubiquinone dehydrogenase (NQR) is a vital component of the respiratory chain of numerous species of marine and pathogenic bacteria,…”
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Simple Entropy Terms for End-Point Binding Free Energy Calculations by Menzer, William M, Li, Chen, Sun, Wenji, Xie, Bing, Minh, David D. L

“…We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average…”
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Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations by Xie, Bing, Nguyen, Trung Hai, Minh, David D. L

“…We demonstrate the feasibility of estimating protein–ligand binding free energies using multiple rigid receptor configurations. On the basis of T4 lysozyme…”
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On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations by Menzer, William M., Xie, Bing, Minh, David D. L.

“…The impact of harmonic restraints on protein heavy atoms and ligand atoms on end‐point free energy calculations is systematically characterized for 54…”
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On the polarization of ligands by proteins by Willow, Soohaeng Yoo, Xie, Bing, Lawrence, Jason, Eisenberg, Robert S, Minh, David D L

“…Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence…”
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Correction to Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange by Nguyen, Trung Hai, Minh, David D. L

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

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

“…Molecular docking can account for receptor flexibility by combining the docking score over multiple rigid receptor conformations, such as snapshots from a…”
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Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling by Spiridon, Laurentiu, Minh, David D. L

“…Compared to fully flexible molecular dynamics, simulations of constrained systems can use larger time steps and focus kinetic energy on soft degrees of…”
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Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange by Nguyen, Trung Hai, Minh, David D. L

“…We investigate the relationship between the number of intermediate thermodynamic states along a pathway and the precision of free energy estimates. With a…”
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Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design by Amaro, Rommie E., Minh, David D. L., Cheng, Lily S., Lindstrom, William M., Olson, Arthur J., Lin, Jung-Hsin, Li, Wilfred W., McCammon, J. Andrew

“…The emergence and continuing global spread of the highly virulent avian influenza H5N1 has raised concerns of a possible human pandemic. Several approved…”
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Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease by Qin, Sanbo, Minh, David D. L, McCammon, J. Andrew, Zhou, Huan-Xiang

“…The internal dynamics of proteins inside of cells may be affected by the crowded intracellular environments. Here, we test a novel approach to simulations of…”
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Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments by Minh, David D. L, McCammon, J. Andrew

“…The nonequilibrium work relation allows for the calculation of equilibrium free energy differences between states based on the exponential average of…”
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Understanding the Hastings Algorithm by Minh, David D. L., Minh, Do Le (Paul)

“…The Hastings algorithm is a key tool in computational science. While mathematically justified by detailed balance, it can be conceptually difficult to grasp…”
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