Author details

Full Name

Tai-Sung Lee

Affiliation

ORCID

Career Start Year

2000

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36622640	AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.		2023
37805934	AmberTools.		2023
36630672	ACES: Optimized Alchemically Enhanced Sampling.		2023
36450130	AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA).	Journal of Chemical Information and Modeling	2022
34521199	CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.	Journal of Chemical Information and Modeling	2021
34029468	Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies.	J Chem Theory Comput	2021
32672455	Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.	J Chem Theory Comput	2020
32175507	Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF.	ACS Omega	2020
32551593	Validation of Free Energy Methods in AMBER.	Journal of Chemical Information and Modeling	2020
32936637	Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.	J Chem Inf Model	2020
32962378	A fast and high-quality charge model for the next generation general AMBER force field.	Journal of Chemical Physics	2020
31244091	Using AMBER18 for Relative Free Energy Calculations.	Journal of Chemical Information and Modeling	2019
30199633	GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.	J Chem Inf Model	2018
28618232	Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration.	Journal of Chemical Theory and Computation	2017
28768099	A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.	Journal of Chemical Theory and Computation	2017
27774349	A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.	ACS Catalysis	2016
27480697	The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and SchrÃ¶dinger FEP.	J Comput Aided Mol Des	2016
26580900	Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.	Journal of Chemical Theory and Computation	2015
25726472	Multiscale methods for computational RNA enzymology.	Methods in Enzymology	2015
26170378	Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.	RNA	2015
24803866	Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods.	Journal of Chemical Theory and Computation	2014
24505217	Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.	Journal of Chemical Theory and Computation	2014
23457427	A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.	Journal of Chemical Theory and Computation	2013
23814506	A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.	Journal of Chemical Theory and Computation	2013
24156941	Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.	Progress in Molecular Biology and Translational Science	2013
23615525	On the regulation and activation of JAK2: a novel hypothetical model.	Molecular Cancer Research	2013
22771572	Mapping L1 ligase ribozyme conformational switch.	Journal of Molecular Biology	2012
21858098	Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.	PLoS One	2011
21266020	Three novel alternative splicing mutations in BCR-ABL1 detected in CML patients with resistance to kinase inhibitors.	Int J Lab Hematol	2011
21379373	Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.	Journal of Chemical Theory and Computation	2011
22200005	Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path.	Journal of Physical Chemistry Letters	2011
20167653	Identification of dynamical hinge points of the L1 ligase molecular switch.	RNA	2010
20812715	Computational mutagenesis studies of hammerhead ribozyme catalysis.	Journal of the American Chemical Society	2010
19195039	Mechanisms of constitutive activation of Janus kinase 2-V617F revealed at the atomic level through molecular dynamics simulations.	Cancer	2009
19265710	Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.	Journal of Molecular Biology	2009
19744331	Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations.	BMC Struct Biol	2009
19519539	Basis for resistance to imatinib in 16 BCR-ABL mutants as determined using molecular dynamics.		2009
18271579	Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.	Journal of the American Chemical Society	2008
19204803	Reverse conservation analysis reveals the specificity determining residues of cytochrome P450 family 2 (CYP 2).	Evolutionary Bioinformatics	2008
19056677	BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations.	Mol Cancer Ther	2008
18479101	Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.	Journal of the American Chemical Society	2008
18338744	Molecular basis explanation for imatinib resistance of BCR-ABL due to T315I and P-loop mutations from molecular dynamics simulations.	Cancer	2008
18420140	Solvent structure and hammerhead ribozyme catalysis.		2008
17442410	Molecular basis of antagonism between K70E and K65R tenofovir-associated mutations in HIV-1 reverse transcriptase.	Antiviral Research	2007
19079784	Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.	Journal of Chemical Theory and Computation	2007
19455225	Multiple property tolerance analysis for the evaluation of missense mutations.	Evolutionary Bioinformatics	2007
16580853	QCRNA 1.0: a database of quantum calculations for RNA catalysis.	J Mol Graph Model	2006
14531054	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.	J Comput Chem	2003
11749542	An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.	Journal of the American Chemical Society	2001
11123888	Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.	Acc Chem Res	2000