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Tai-Sung Lee

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Position: Associate Research Professor
Education:
Duke University - Ph.D. Theoretical Chemistry (1997), National Taiwan University - M.S. Analytical Chemistry - NMR (1990)
Email: taisung[at]rutgers.edu
Office: CIPR-308E


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.





Publications:

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020)
DOI: 10.1021/acs.jcim.0c00613
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Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) 16, 5512-5525
DOI: 10.1021/acs.jctc.0c00237
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Validation of Free Energy Methods in AMBER

(2020)
DOI: 10.1021/acs.jcim.0c00285
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Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein−Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

(2020) 5, 4611-4619
DOI: 10.1021/acsomega.9b04233
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Using AMBER18 for Relative Free Energy Calculations

(2019) 59, 3128-3135
DOI: 10.1021/acs.jcim.9b00105
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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) 58, 2043-2050
DOI: 10.1021/acs.jcim.8b00462
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A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations

(2017) 13, 3975-3984
DOI: 10.1021/acs.jctc.7b00161
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Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

(2017) 13, 3077-3084
DOI: 10.1021/acs.jctc.7b00102
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A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

(2016) 6, 1853-1869
DOI: 10.1021/acscatal.5b02158
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The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

(2016) 30, 533-539
DOI: 10.1007/s10822-016-9920-5
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Multiscale methods for computational RNA enzymology

(2015) 553, 335-374
ISBN: 12345
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Assessment of Metal-Assisted Nucleophile Activation in the Hepatitis Delta Virus Ribozyme from Molecular Simulation and 3D-RISM

(2015) 21, 1-12
DOI: 10.1261/rna.051466.115
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Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

(2015) 11, 373-377
DOI: 10.1021/ct500776j
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Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods

(2014) 10, 1538–1545
DOI: 10.1021/ct401013s
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Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach

(2014) 10, 24-34
DOI: 10.1021/ct400691f
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Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis

(2013) 120, 25-91
ISBN: 12345
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A Framework for Flexible and Scalable Replica-Exchange on Production Distributed Cyberinfrastructure.

(2013)
ISBN: 12345
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A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields

(2013) 9, 1417-1427
DOI: 10.1021/ct3010134
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A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2013) 9, 153-164
DOI: 10.1021/ct300703z
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Mapping L1 ligase ribozyme conformational switch

(2012) 423, 106-122
DOI: 10.1016/j.jmb.2012.06.035
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Characterization of the structure and dynamics of the HDV ribozyme in different stages along the reaction path

(2011) 2, 2538-2543
DOI: 10.1021/jz201106y
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Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozymes

(2011) 7, 1-3
DOI: 10.1021/ct100467t
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Computational mutagenesis studies of hammerhead ribozyme catalysis

(2010) 132, 13505-13518
DOI: 10.1021/ja105956u
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Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations

(2010) 6, 168-200
ISBN: 12345
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Identification of dynamical hinge points of the L1 ligase molecular switch

(2010) 16, 769-780
DOI: 10.1261/rna.1897810
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Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations

(2009) 7, 377-408
ISBN: 12345
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Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation

(2009) 388, 195-206
DOI: 10.1016/j.jmb.2009.02.054
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Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations

(2008) 130, 7168-7169
DOI: 10.1021/ja711242b
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Solvent structure and hammerhead ribozyme catalysis

(2008) 15, 332-342
DOI: 10.1016/j.chembiol.2008.03.010
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Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

(2008) 130, 3053-3064
DOI: 10.1021/ja076529e
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Insight into the role of Mg2+in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation

(2007) 3, 325-327
DOI: 10.1021/ct6003142
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QCRNA 1.0: A database of quantum calculations for RNA catalysis

(2006) 25, 423-433
DOI: 10.1016/j.jmgm.2006.02.011
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Quantum Mechanical Treatment of Biological Macromolecules in Solution using Linear-Scaling Electronic Structure Methods

(1998) 80, 5011-5014
DOI: 10.1103/PhysRevLett.80.5011
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Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules

(1996) 263, 297-304
DOI: 10.1016/S0009-2614(96)01198-0
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Quantum Mechanical Study of Aqueous Polarization Effects on Biological Macromolecules

(1996) 118, 10940-10941
DOI: 10.1021/ja961937w
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Linear-scaling semiempirical quantum calculations for macromolecules

(1996) 105, 2744
DOI: 10.1063/1.472136
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A new definition of atomic charges based on a variational principle for the electrostatic potential energy

(1995) 102, 7549
DOI: 10.1063/1.469086
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