List of works - Tai-Sung Lee

A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations

scientific article

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

scientific article published on 12 December 2012

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

scientific article (publication date: 2016)

A fast and high-quality charge model for the next generation general AMBER force field

scientific article published on 01 September 2020

A framework for flexible and scalable replica-exchange on production distributed CI

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

scientific article published on 16 September 2020

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

scientific article

BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations

scientific article

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

scientific article

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

scientific article published on October 2011

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

scientific article published on February 2015

Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis ⬇️

scientific article published on September 29, 2010

Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling ⬇️

scientific article published on August 17, 2011

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

scientific article published on 25 February 2020

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

scientific article published on 25 September 2018

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

scientific article published on 16 July 2020

Molecular basis explanation for imatinib resistance of BCR-ABL due to T315I and P-loop mutations from molecular dynamics simulations

scientific article

Multiscale methods for computational RNA enzymology.

scientific article published on 22 January 2015

On the regulation and activation of JAK2: a novel hypothetical model

scientific article

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach

scientific article published on January 2014

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

scientific article published on 14 February 2008

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

scientific article published on 24 May 2021

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

scientific article published in August 2016

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

scientific article published on 15 June 2017

Using AMBER18 for Relative Free Energy Calculations

scientific article published on 20 June 2019

Validation of Free Energy Methods in AMBER

scientific article published on 18 June 2020

List of works by Tai-Sung Lee

A Multi-dimensional B-spline Method for Accurate Modeling Sugar Puckering in QM/MM Simulations

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation

A fast and high-quality charge model for the next generation general AMBER force field

A framework for flexible and scalable replica-exchange on production distributed CI

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

Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.

BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path

Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations

Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis ⬇️

Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling ⬇️

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

Molecular basis explanation for imatinib resistance of BCR-ABL due to T315I and P-loop mutations from molecular dynamics simulations

Multiscale methods for computational RNA enzymology.

On the regulation and activation of JAK2: a novel hypothetical model

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach

Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation

Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

Using AMBER18 for Relative Free Energy Calculations

Validation of Free Energy Methods in AMBER