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David Minh

David Minh, Ph.D.

David Minh, Ph.D.
Assistant Professor of Chemistry

Phone: 

312.567.3147

Education 

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

Research & Accomplishments 

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

  1. 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.
  2. 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.

Expertise 

Computational Chemical Biology and Structure-Based Drug Design

Theoretical Chemistry, especially Statistical Mechanics

Biophysical Chemistry

Publications 

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

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

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

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

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

Minh DDL, Chang CE, Trylska J, Tozzini V, and McCammon JA. The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc, 128(18): 6006-6007 (2006). doi:10.1021/ja060483s

Minh DDL, Bui JM, Chang CE, Jain T, Swanson JM, McCammon JA. The entropic cost of protein-protein association: a case study on acetylcholinesterase binding to fasciculin-2. Biophys J, 89(4):L25-7 (2005). doi:10.1529/biophysj.105.069336