Ph.D. University of California, San Diego M.S. University of California, San Diego B.A. University of California, Berkeley

The primary research interests of the David Minh group are to:

Develop new computational methods to quickly and accurately characterize protein-ligand interactions, especially binding affinities. These structure-based methods are built upon a rigorous foundation of statistical mechanics. Apply these methods to design specific chemical probes for biological processes. In some cases, these probes may become drug leads. We are also interested in statistical mechanics, both in- and out-of-equilibrium. Of particular interest are stochastic sampling algorithms based on Monte Carlo and molecular dynamics.

Recently, David derived implicit ligand theory, a new framework for estimating binding free energies of noncovalent association. Unlike previous theories, implicit ligand theory is based on multiple rigid configurations of the receptor. In principle, freezing receptor atoms allows for computational efficiency gains that could make binding free energy calculations nearly as fast as molecular docking calculations (which are speedy but relatively inaccurate). Much effort in the group is directed towards turning this potential into reality.

Ultimately, we plan to apply these methods to designing inhibitors for protein-protein interactions, developing a quantitative understanding of functional selectivity in G-protein coupled receptors, and predicting the selectivity of kinase inhibitors, among other purposes. We are open to collaborative opportunities.

Minh DDL, Makowski L. Wide-angle X-ray solution scattering for protein-ligand binding: Multivariate curve resolution with Bayesian confidence intervals. Biophysical Journal, 104: 873-883 (2013). doi:10.1016/j.bpj.2012.12.019

Minh DDL. Implicit Ligand Theory: Rigorous binding free energies and thermodynamic expectations from molecular docking. J Chem Phys, 137: 104106 (2012). doi:10.1063/1.4751284

Minh DDL. Comment on “Transient-state fluctuationlike relation for the driving force on a biomolecule”. Phys Rev E, 85: 053103 (2012). doi:10.1103/PhysRevE.85.053103

Minh DL, Minh DDL, Nguyen L. Regenerative Markov Chain Monte Carlo for Any Distribution, Comm Stat Simulat Comput, 41(9):1745-1760 (2012). doi:10.1080/03610918.2011.615433

Nilmeier JP, Crooks GE, Minh DDL, Chodera JD. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation, Proc Natl Acad Sci USA, 108(45):E1009-1018 (2011). doi:10.1073/pnas.1106094108

Makowski L, Gore D, Mandava S, Minh DDL, Park S, Rodi, DJ, and Fischetti RF. X‐ray solution scattering studies of the structural diversity intrinsic to protein ensembles. Biopolymers, 95: 531-542 (2011). doi:10.1002/bip.21631

Minh DDL, Vaikuntanathan S. Density-Dependent Analysis of Nonequilibrium Paths Improves Free Energy Estimates II. A Feynman-Kac Formalism. J Chem Phys, 134(3): 034117 (2011). doi:10.1063/1.3541152

Minh DDL, Chodera JD. 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. J Chem Phys, 134(2): 024111 (2011). doi:10.1063/1.3516517

Minh DDL. Optimized replica gas estimation of absolute integrals and partition functions. Phys Rev E, 82(3): 031132 (2010). doi:10.1103/PhysRevE.82.031132

Qin S, Minh DDL, McCammon JA, Zhou, HX. Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease. J Phys Chem Lett, 1(1):107–110 (2010). doi:10.1021/jz900023w

Minh DDL, Chodera JD. Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J Chem Phys, 131(13): 134110 (2009). doi:10.1063/1.3242285

Minh DDL. Density-Dependent Analysis of Nonequilibrium Paths Improves Free Energy Estimates. J Chem Phys, 130(20): 204102 (2009). doi:10.1063/1.3139189

Minh DDL, Adib AB. Path integral analysis of Jarzynski’s equality: Analytical results. Phys Rev E, 79(2): 021122 (2009). doi: 10.1103/PhysRevE.79.021122

Minh DDL, McCammon JA. Springs and Speeds in Free Energy Reconstruction from Nonequilibrium Single-Molecule Pulling Experiments. J Phys Chem B, 112(19): 5892-5897 (2008). doi:10.1021/jp0733163

Minh DDL, Adib AB. Optimized free energies from bidirectional single-molecule force spectroscopy. Phys Rev Lett, 100(18): 180602 (2008). doi:10.1103/PhysRevLett.100.180602

Makowski L, Rodi DJ, Mandava S, Minh DDL, Gore DB, Fischetti RF. Molecular Crowding Inhibits Intramolecular Breathing Motions in Proteins. J Mol Biol, 375(2): 529-546 (2008). doi:10.1016/j.jmb.2007.07.075

Minh DDL, Hamelberg D, McCammon JA. Accelerated Entropy Estimates with Accelerated Dynamics. J Chem Phys, 127(15):154105 (2007). doi:10.1063/1.2794754

Amaro R, Minh DDL, Cheng L, Lindstrom WM, Olson AJ, Lin JH, Olson AJ, McCammon JA. Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antiviral Drug Design. J Am Chem Soc, 129(25):7764-7765 (2007). doi:10.1021/ja0723535

Minh DDL. Multidimensional Potentials of Mean Force from Biased Experiments Along a Single Coordinate. J Phys Chem B, 111(16): 4137-4140 (2007). doi:10.1021/jp068656n

Minh DDL. Free Energy Reconstruction from Experiments Performed Under Different Biasing Programs. Phys Rev E, 74(6): 061120 (2006). doi:10.1103/PhysRevE.74.061120