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Tai-Sung Lee

Associate Research Professor
Duke University - Ph.D. Theoretical Chemistry (1997)
National Taiwan University - M.S. Analytical Chemistry, NMR (1990)
taisung [at]
cancersimulation [at]
About Me: 

My research interests are in the following three directions:

    • Multi-scale molecular simulation methodological development and software implementations:
      • Maximum-likelihood based free energy methods.
      • Service-oriented integration of modeling software modules.
    • Cancer related modeling and simulation:
      • JAK2 regulation and activation mechanisms.
      • EpoR/TpoR signaling mechanisms.
    • Ribozyme conformation and reaction simulation:
      • HDV ribozyme.
      • HHR ribozyme.

My Webpage

Lee Publications

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP
Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations
Multiscale methods for computational RNA enzymology
Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM
Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods
Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis
A Framework for Flexible and Scalable Replica-Exchange on Production Distributed Cyberinfrastructure.
Mapping l1 ligase ribozyme conformational switch
Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes
Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path
Identification of dynamical hinge points of the L1 ligase molecular switch
Insights into the Role of Conformational Transitionsand Metal Ion Binding in RNA Catalysis from Molecular Simulations
Computational mutagenesis studies of hammerhead ribozyme catalysis
Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation
Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations
Solvent structure and hammerhead ribozyme catalysis
Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
Insight into the role of Mg2+ in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation
QCRNA 1.0: A database of quantum calculations for RNA catalysis
Quantum Mechanical Treatment of Biological Macromolecules in Solution Using Linear-Scaling Electronic Structure Methods
Linear‐scaling semiempirical quantum calculations for macromolecules
Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules
Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules
A new definition of atomic charges based on a variational principle for the electrostatic potential energy