Jump to CCB Lab publications or David’s prior work. Also see David’s profile on ResearcherID or ORCID.
On Inactivation of the Coronavirus Main Protease
HH Nguyen; J Tufts; DDL Minh
Journal of Chemical Information and Modeling , acs.jcim.3c01518 (2024)
Open Science Discovery of Potent Noncovalent SARS-CoV-2 Main Protease Inhibitors
ML Boby; D Fearon; M Ferla; M Filep; L Koekemoer; MC Robinson; {The COVID Moonshot Consortium{\ddag}}; JD Chodera; AA Lee; N London; A Von Delft; F Von Delft; H Achdout; A Aimon; DS Alonzi; R Arbon; JC Aschenbrenner; BH Balcomb; E {Bar-David}; H Barr; A {Ben-Shmuel}; J Bennett; VA Bilenko; B Borden; P Boulet; GR Bowman; L Brewitz; J Brun; S Bvnbs; M Calmiano; A Carbery; DW Carney; E Cattermole; E Chang; E Chernyshenko; A Clyde; JE Coffland; G Cohen; JC Cole; A Contini; L Cox; TI Croll; M Cvitkovic; S De Jonghe; A Dias; K Donckers; DL Dotson; A Douangamath; S Duberstein; T Dudgeon; LE Dunnett; P Eastman; N Erez; CJ Eyermann; M Fairhead; G Fate; O Fedorov; RS Fernandes; L Ferrins; R Foster; H Foster; L Fraisse; R Gabizon; A {Garc{'i}a-Sastre}; VO Gawriljuk; P Gehrtz; C Gileadi; C Giroud; WG Glass; RC Glen; I Glinert; AS Godoy; M Gorichko; T {Gorrie-Stone}; EJ Griffen; A Haneef; S Hassell Hart; J Heer; M Henry; M Hill; S Horrell; QYJ Huang; VD Huliak; MFD Hurley; T Israely; A Jajack; J Jansen; E Jnoff; D Jochmans; T John; B Kaminow; L Kang; AL Kantsadi; PW Kenny; JL Kiappes; SO Kinakh; B Kovar; T Krojer; VNT La; S {Laghnimi-Hahn}; BA Lefker; H Levy; RM Lithgo; IG Logvinenko; P Lukacik; HB Macdonald; EM MacLean; LL Makower; TR Malla; PG Marples; T Matviiuk; W McCorkindale; BL McGovern; S Melamed; KP Melnykov; O Michurin; P Miesen; H Mikolajek; BF Milne; D Minh; A Morris; GM Morris; MJ Morwitzer; D Moustakas; CE Mowbray; AM Nakamura; JB Neto; J Neyts; L Nguyen; GD Noske; V Oleinikovas; G Oliva; GJ Overheul; CD Owen; R Pai; J Pan; N Paran; AM Payne; B Perry; M Pingle; J Pinjari; B Politi; A Powell; V P{\v s}enák; I Pulido; R Puni; VL Rangel; RN Reddi; P Rees; SP Reid; L Reid; E Resnick; EG Ripka; RP Robinson; J {Rodriguez-Guerra}; R Rosales; DA Rufa; K Saar; KS Saikatendu; E Salah; D Schaller; J Scheen; CA Schiffer; CJ Schofield; M Shafeev; A Shaikh; AM Shaqra; J Shi; K Shurrush; S Singh; A Sittner; P Sj{"o}; R Skyner; A Smalley; B Smeets; MD Smilova; LJ Solmesky; J Spencer; C {Strain-Damerell}; V Swamy; H Tamir; JC Taylor; RE Tennant; W Thompson; A Thompson; S Tomásio; CWE Tomlinson; IS Tsurupa; A Tumber; I Vakonakis; RP Van Rij; L Vangeel; FS Varghese; M Vaschetto; EB Vitner; V Voelz; A Volkamer; MA Walsh; W Ward; C Weatherall; S Weiss; KM White; CF Wild; KD Witt; M Wittmann; N Wright; Y {Yahalom-Ronen}; NK Yilmaz; D Zaidmann; I Zhang; H Zidane; N Zitzmann; SN Zvornicanin
Science 382, eabo7201 (2023)
Inclusion of Control Data in Fits to Concentration–Response Curves Improves Estimates of Half-Maximal Concentrations
VNT La; S Nicholson; A Haneef; L Kang; DDL Minh
Journal of Medicinal Chemistry 66, 12751–12761 (2023)
Bayesian Regression Quantifies Uncertainty of Binding Parameters from Isothermal Titration Calorimetry More Accurately Than Error Propagation
VNT La; DDL Minh
International Journal of Molecular Sciences 24, 15074 (2023)
H-Bonds in Crambin: Coherence in an {$\alpha$}-Helix
S Nicholson; DDL Minh; R Eisenberg
ACS Omega 8, 13920–13934 (2023)
Learned Mappings for Targeted Free Energy Perturbation between Peptide Conformations
SY Willow; L Kang; DDL Minh
Journal of Chemical Physics 159, 124104 (2023)
Bayesian Regression and Model Selection for Isothermal Titration Calorimetry with Enantiomeric Mixtures
TH Nguyen; VNT La; K Burke; DDL Minh
PLoS ONE 17, e0273656 (2022)
Identification of the Riboflavin Cofactor-Binding Site in the Vibrio Cholerae Ion-Pumping NQR Complex: A Novel Structural Motif in Redox Enzymes
K Tuz; M Yuan; Y Hu; TTT Do; SY Willow; JA {DePaolo-Boisvert}; JR Fuller; DDL Minh; O Juárez
Journal of Biological Chemistry 298, 102182 (2022)
Electrostatics and Water Occlusion Regulate Covalently-bound Flavin Mononucleotide Cofactors of Vibrio Cholerae Respiratory Complex NQR
SY Willow; M Yuan; O Juárez; DDL Minh
Proteins: Structure, Function, and Bioinformatics 89, prot.26158 (2021)
On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations
WM Menzer; B Xie; DDL Minh
Journal of Computational Chemistry 41, 573–586 (2020)
Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
DDL Minh
Journal of Computational Chemistry 41, 715–730 (2020)
Implicit Ligand Theory for Relative Binding Free Energies: II. An Estimator Based on Control Variates
TH Nguyen; DDL Minh
Journal of Physics Communications 4, 115010 (2020)
Robosample: Rigid-body Molecular Simulation Based on Robot Mechanics
L Spiridon; TA Sulea; DDL Minh; AJ Petrescu
BBA - General Subjects 1864, 129616 (2020)
On the Polarization of Ligands by Proteins
SY Willow; B Xie; J Lawrence; RS Eisenberg; DDL Minh
Physical Chemistry Chemical Physics 22, 12044–12057 (2020)
A Structural Model for BaxΔ2-Mediated Activation of Caspase 8-Dependent Apoptosis
B Xie; Q Yao; J Xiang; DDL Minh
International Journal of Molecular Sciences 21, 5476 (2020)
Conserved Residue His-257 of Vibrio Cholerae Flavin Transferase ApbE Plays a Critical Role in Substrate Binding and Catalysis
X Fang; J Osipiuk; S Chakravarthy; M Yuan; W Menzer; D Nissen; P Liang; DA Raba; K Tuz; AJ Howard; A Joachimiak; DDL Minh; O Juárez
Journal of Biological Chemistry 294, 13800–13810 (2019)
Nonequilibrium Path-Ensemble Averages for Symmetric Protocols
TH Nguyen; V Ngo; J Castro Zerba; SY Noskov; DDL Minh
Journal of Chemical Physics 151, 194103 (2019)
Role of Subunit D in Ubiquinone-Binding Site of Vibrio Cholerae NQR: Pocket Flexibility and Inhibitor Resistance
DA Raba; M Yuan; X Fang; WM Menzer; B Xie; P Liang; K Tuz; DDL Minh; O Juárez
ACS Omega 4, 19324–19331 (2019)
Alchemical Grid Dock (AlGDock) Calculations in the D3R Grand Challenge 3
B Xie; DDL Minh
Journal of Computer-Aided Molecular Design 33, 61–69 (2019)
Simple Entropy Terms for End-Point Binding Free Energy Calculations
W Menzer; C Li; W Sun; B Xie; DDL Minh
Journal of Chemical Theory and Computation 14, 6035–6049 (2018)
Power Transformations Improve Interpolation of Grids for Molecular Mechanics Interaction Energies
DDL Minh
Journal of Computational Chemistry 39, 1200–1207 (2018)
Using the Fast Fourier Transform in Binding Free Energy Calculations
TH Nguyen; H Zhou; DDL Minh
Journal of Computational Chemistry 39, 621–636 (2018)
Bayesian Analysis of Isothermal Titration Calorimetry for Binding Thermodynamics
TH Nguyen; AS Rustenburg; SG Krimmer; H Zhang; JD Clark; PA Novick; K Branson; VS Pande; JD Chodera; DDL Minh
PLoS ONE 13, e0203224 (2018)
Implicit Ligand Theory for Relative Binding Free Energies
TH Nguyen; DDL Minh
Journal of Chemical Physics 148, 104114 (2018)
Characterization of the Pseudomonas Aeruginosa NQR Complex, a Bacterial Proton Pump with Roles in Autopoisoning Resistance
DA Raba; M {Rosas-Lemus}; WM Menzer; C Li; X Fang; P Liang; K Tuz; DDL Minh; O Juárez
Journal of Biological Chemistry 293, 15664–15677 (2018)
Design, Synthesis, and Biological Evaluation of Novel Polyaminocarboxylate Ligand-Based Theranostic Conjugate for Antibody-Targeted Cancer Therapy and Near-Infrared Optical Imaging
S Ren; X Sun; H Wang; TH Nguyen; N Sadeghipour; X Xu; CS Kang; Y Liu; H Xu; N Wu; Y Chen; K Tichauer; DDL Minh; H Chong
ChemMedChem 13, 2606–2617 (2018)
Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles
B Xie; JD Clark; DDL Minh
Journal of Chemical Information and Modeling 58, 1915–1925 (2018)
Effects of Catalytic Action and Ligand Binding on Conformational Ensembles of Adenylate Kinase
E Onuk; J Badger; YJ Wang; J Bardhan; Y Chishti; M Akcakaya; DH Brooks; D Erdogmus; DDL Minh; L Makowski
Biochemistry 56, 4559–4567 (2017)
Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling
L Spiridon; DDL Minh
Journal of Chemical Theory and Computation 13, 4649–4659 (2017)
Identification of the Catalytic Ubiquinone-binding Site of Vibrio Cholerae Sodium-dependent NADH Dehydrogenase: A NOVEL UBIQUINONE-BINDING MOTIF
K Tuz; C Li; X Fang; DA Raba; P Liang; DDL Minh; O Juárez
Journal of Biological Chemistry 292, 3039–3048 (2017)
Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations
B Xie; TH Nguyen; DDL Minh
Journal of Chemical Theory and Computation 13, 2930–2944 (2017)
Layer Sampling
DDL Minh; DL Minh; AL Nguyen
Communications in Statistics - Simulation and Computation 45, 73–100 (2016)
Intermediate Thermodynamic States Contribute Equally to Free Energy Convergence: A Demonstration with Replica Exchange
TH Nguyen; DDL Minh
Journal of Chemical Theory and Computation 12, 2154–2161 (2016)
Understanding the Hastings Algorithm
DDL Minh; DL Minh
Communications in Statistics - Simulation and Computation 44, 332–349 (2015)
Wide-Angle X-ray Solution Scattering for Protein-Ligand Binding: Multivariate Curve Resolution with Bayesian Confidence Intervals
DDL Minh; L Makowski
Biophysical Journal 104, 873–883 (2013)
Implicit Ligand Theory: Rigorous Binding Free Energies and Thermodynamic Expectations from Molecular Docking
DDL Minh
Journal of Chemical Physics 137, 104106 (2012)
Comment on ``Transient-state Fluctuationlike Relation for the Driving Force on a Biomolecule’’
DDL Minh
Physical Review E 85, 053103 (2012)
Regenerative Markov Chain Monte Carlo for Any Distribution
DL Minh; DDL Minh; AL Nguyen
Communications in Statistics - Simulation and Computation 41, 1745–1760 (2012)
X-Ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles
L Makowski; DB Gore; S Mandava; DDL Minh; S Park; DJ Rodi; RF Fischetti
Biopolymers 95, 531–542 (2011)
Estimating Equilibrium Ensemble Averages Using Multiple Time Slices from Driven Nonequilibrium Processes: Theory and Application to Free Energies, Moments, and Thermodynamic Length in Single-Molecule Pulling Experiments
DDL Minh; JD Chodera
Journal of Chemical Physics 134, 024111 (2011)
Density-Dependent Analysis of Nonequilibrium Paths Improves Free Energy Estimates II. A Feynman-Kac Formalism
DDL Minh; S Vaikuntanathan
Journal of Chemical Physics 134, 034117 (2011)
PNAS Plus: Nonequilibrium Candidate Monte Carlo Is an Efficient Tool for Equilibrium Simulation
JP Nilmeier; GE Crooks; DDL Minh; JD Chodera
Proceedings of the National Academy of Sciences of the United States of America 108, E1009-E1018 (2011)
Optimized Replica Gas Estimation of Absolute Integrals and Partition Functions
DDL Minh
Physical Review E 82, 31132 (2010)
Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease
SB Qin; DDL Minh; JA McCammon; HX Zhou
Journal of Physical Chemistry Letters 1, 107–110 (2010)
Density-Dependent Analysis of Nonequilibrium Paths Improves Free Energy Estimates
DDL Minh
Journal of Chemical Physics 130, 204102 (2009)
Path Integral Analysis of Jarzynski’s Equality: Analytical Results
DDL Minh; AB Adib
Physical Review E 79, 021122 (2009)
Optimal Estimators and Asymptotic Variances for Nonequilibrium Path-Ensemble Averages
DDL Minh; JD Chodera
Journal of Chemical Physics 131, 134110 (2009)
Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins
L Makowski; DJ Rodi; S Mandava; DDL Minh; DB Gore; RF Fischetti
Journal of Molecular Biology 375, 529–546 (2008)
Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy
DDL Minh; AB Adib
Physical Review Letters 100, 180602 (2008)
Springs and Speeds in Free Energy Reconstruction from Irreversible Single-Molecule Pulling Experiments
DDL Minh; JA McCammon
Journal of Physical Chemistry B 112, 5892–5897 (2008)
Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design
RE Amaro; DDL Minh; LS Cheng; J Lindstrom William M; AJ Olson; JH Lin; WW Li; JA McCammon
Journal of the American Chemical Society 129, 7764–7765 (2007)
Multidimensional Potentials of Mean Force from Biased Experiments along a Single Coordinate
DDL Minh
Journal of Physical Chemistry B 111, 4137–4140 (2007)
Accelerated Entropy Estimates with Accelerated Dynamics
DDL Minh; D Hamelberg; JA McCammon
Journal of Chemical Physics 127, 154105 (2007)
Free-Energy Reconstruction from Experiments Performed under Different Biasing Programs
DDL Minh
Physical Review E 74, 61120 (2006)
The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics
DDL Minh; CA Chang; J Trylska; V Tozzini; JA McCammon
Journal of the American Chemical Society 128, 6006–6007 (2006)
The Entropic Cost of Protein-Protein Association: A Case Study on Acetylcholinesterase Binding to Fasciculin-2
DDL Minh; JM Bui; C Chang; T Jain; JMJ Swanson; JA McCammon
Biophysical Journal 89, L25-L27 (2005)
