Publications
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Edited Book:
“Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications”
Darrin M. York and Tai-Sung Lee, editors, Springer Verlag, 2009.
as part of the book series: “Challenges and Advances in Computational Chemistry and Physics”, with series editor Jerzy Leszcynski, and published by Springer Verlag (2007).
The purpose of this book is to provide a modern perspective of current state-of-the-art methods for the multi-scale modeling of biocatalysis, and they types of problems that can be addressed by these techniques.
Journal articles (current h-index: 21): (corresponding author: 15 (underlined); first author: 33)
51. Radak, K. B., Lee, T.-S., He, P., et al“ A framework for flexible and scalable replica-exchange on production distributed CI”
50. Lee, T. –S.“ On the negative regulation and activation of JAK2: A novel hypothetical model”
Molecular Cancer Research, 2013, 11:811-814, perspective article.
49. Giese, I. et al, “A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields”
Journal of Chemical Theory and Computation, 2013, 9: 1417-1427
48. Lee, T. –S., Radak, B..K.; Pabis A.; York, D. M., “A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations”
Journal of Chemical Theory and Computation, 2013, 9:153-164
47. Giambasu, G. M.; Lee, T. –S.; Scott, W. G.; York D. M., “Mapping L1 Ligase ribozyme conformational switch”
Journal of Molecular Biology, 2012, 2:106-122
46. Lee, T.-S.; Giambasu, G. M.; Harris, M. E.; York, D. M., “Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path”,
The Journal of Physical Chemistry Letters, 2011, 2:2538-2543
45. Lee, T. –S. ; Kantarjian, H.; Ma, W.; Yeh, C.-H.; Cortes, J.; Albitar, M., “Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling”,
44. Ma, W.; Giles, F.; Zhang, X.; Wang, X.; Zhang, Z.; Lee, T-S.; Yeh, C-H.; Albitar, M., “Three novel alternative splicing mutations in BCR-ABL1 detected in CML patients with resistance to kinase inhibitors””,
International Journal of Laboratory Hematology 2011, 33:326-331
43. Wong, K. -Y.; Lee, T. –S.; York D. M., “Active participation of Mg2+ ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme”
Journal of Chemical Theory and Computation (comm.), 2011, 7:1-3.
42. Lee, T.-S.; Giambasu, G. M.; York, D. M., “Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations”
41. Lee, T.-S.; York, D. M. "Computational mutagenesis studies of hammerhead ribozyme catalysis."
Journal of the American Chemical Society, 2010, 132: 13505-13518.
40. Lee, T.-S.; Giambasu, G. M. York, D. M.,“Insights into the role of conformational transitions and metal ion binding in RNA catalysis from molecular simulations.” in
Annual Reports in Computational Chemistry, 6:168-200, A. W. Ralph, Ed.; Elsevier. 2010
39. Lee, T. –S.; Ma, W.; Zhang, X.; Giles. F.; Cortes, J.; Kantarjian, H.; Albitar, M.,“BCR-ABL1INS35 is not uncommon in CML patients and is related to resistance and sensitivity to inhibitors in CML treatment””,
Molecular Cancer Therapeutics, 2010, 9:772.
38. Giambasu, G. M.; Lee, T. –S.; Sosa, C.P.; Robertson, M.P.; Scott, W. G.; York D. M., “Identification of dynamical hinge points of the L1 ligase molecular switch”
37. Lee, T. –S.; Ma, W.; Zhang, X.; Kantarjian, H.; Albitar, M.,“Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations”
BMC Structural Biology, 2009, 9:58-71
36. Lee, T. –S.; Giambasu, G. M.; Sosa, C.; Scott, W.G.; York D. M., “Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active in-line conformation”
Journal of Molecular Biology, 2009, 388:195-206
35. Lee, T. –S.; Potts, S. J.; Albitar, M., “Basis for resistance to imatinib in 16 BCR-ABL mutants as determined using molecular dynamics”
Recent Patents on Anti-Cancer Drug Discovery, 2009, 4:164-73.
34. Lee, T. –S.; Giambasu, G.M.; Nam, K.; Guerra, F.; Giese, T. J.; York, D. M., "Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations", (book chapter) in
“Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications”, York D. M. and Lee, T. –S. , (Editors), Springer Verlag, New York, 2009.
33. Lee, T. –S.; Ma, W.; Zhang, X.; Giles. F.; Kantarjian, H.; Albitar, M., “Mechanisms of constitutive activation of JAK2-V617F revealed at the atomic Level through molecular dynamics simulations”,
32. Lee, T. –S.; Ma, W.; Zhang, X.; Giles. F.; Cortes, J.; Kantarjian, H.; Albitar, M., “BCR-ABL alternative-splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations”,
Molecular Cancer Therapeutics, 2008, 7:3834-3841.
31. Lee, T. –S. and York D. M., “Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations”,
Journal of the American Chemical Society (communication), 2008, 130: 7168-7169.
30. Martick, M.; Lee, T. –S.; York, D. M.; Scott, W., “Solvent structure and hammerhead ribozyme catalysis”,
Chemistry & Biology, 2008, 15:332-342.
29. Lee, T. –S.; Silva-López, C. , Martick, M.; Scott, W.G.; York D. M., “Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation”,
Journal of the American Chemical Society, 2008, 130:3053 -3064
28. Lee, T. –S.; Potts, S. J.; Kantarjian, H.; Cortes, J.; Giles. F.; Albitar, M., “Molecular basis explanation of imatinib resistance of BCR-ABL due to T315I and P-Loop mutations from molecular dynamics simulations”,
27. Lee, T. –S.,“Reverse conservation analysis reveals the specificity determining residues of cytochrome P450 Family 2 (CYP 2)”,
Evolutionary Bioinformatics, 2008, 4:7-16
26. Kagan, R.M.; Lee, T. –S.; Ross, L.; Lloyd Jr.; R.M.; Lewinski, M.A.; Potts, S.J., “Molecular basis of antagonism between K70E and K65R tenofovir-associated mutations in HIV-1 reverse transcriptase”,
Antiviral Research, 2007, 75:210-218
25. Lee, T. –S.; Silva-López, C. , Martick, M.; Scott, W.G.; York D. M., “Insight into the role of Mg2+ in hammerhead ribozyme catalysis from x-ray crystallography and molecular dynamics simulation”,
Journal of Chemical Theory and Computation, 2007, 3:325-327 (Communication).
24. Lee, T. –S.; Potts, S. J.; Mcginniss, M. J.; Strom, C.M.; “Multiple property tolerance analysis for ehe evaluation of missense mutations”
Evolutionary Bioinformatics, 2006, 2:345-356.
23. Lee, T. –S.; et al, “QCRNA 1.0: a database of quantum calculations for RNA catalysis”
Journal of Molecular Graphics and Modeling, 2006, 25, 423-433.
22. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.-S.; Caldwell, J.; Wang, J.; Kollman, P. A.,“A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations”
Journal of Computational Chemistry, 2003, 24:1999-2012.
21. Lee, T. –S., “Fast solvent accessible surface calculation based on fullerene-like grid points”, Accelrys’ Internal Communication, 2002. (The algorithm is used in the DSModeling 1.1 Product.)
20. Lee, T. –S.*, Chong, L. T.*, Chodera , J. and Kollman, P. A., “An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase” (*first two authors contributed equally to the work)
Journal of the American Chemical Society, 2001, 123: 12837-12848.
19. Lee, T. –S. ; Kollman, P.A., “Thymidylate synthase: free energy calculations for estimating inhibitor binding affinities” in
18. Kollman, P.A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.-S.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., ”Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models”,
Accounts of Chemical Research, 2000, 33:889-897.
17. Lee, T.-S.; Massova, I.; Kuhn, B.; Kollman, P. A., “QM and QM-FE simulations on reactions of relevance to enzyme catalysis: trypsin, COMT, b-lactamase and pseudouridine synthetase”,
Journal of Chemical Society Perkin Trans. 2, 2000, 3:409-415.
16. Lee, T.-S.; Kollman, P. A., “Theoretical studies suggest a new antifolate as a more potent inhibitor of thymidylate synthase”
Journal of the American Chemical Society, .2000, 122: 4385-4393.
15. Lee, T.-S.; Kollman, P. A., “Quantum calculations of the nucleophilic attack in tRNA pseudouridine synthesis”,
Journal of the American Chemical Society, 1999, 121: 9928-9931.
14. Robles, J.; Mayorga, O.; Lee, T. -S.; Díaz, D., “PM3 semiempirical electronic structure calculation of capped and uncapped CdS nanoparticles “,
Nanostructured Materials, 1999, 11:283-286.
13. Lewis, J.P.; Liu, S.; Lee, T.-S.; Yang, W, “A linear-scaling quantum mechanical investigation of cytidine deaminase.”
Journal of Computational Physics, 1999, 151:242-263
12. Lee, T.-S.; Lewis, J.P.; Yang, W., “Linear-scaling quantum mechanical calculations of biological molecules: the divide-and-conquer approach.”
Computational Materials Science, 1998, 12:259-277.
11. Zhang, Y.; Lee, T.-S.; Yang, W., “A pseudobond approach to combine quantum mechanical and molecular mechanical methods.”
Journal of Chemical Physics, 1999, 110 :46-54.
10. Lee, T.-S. and Yang, W., “Frozen density matrix approach for electronic structure salculations”
International Journal of Quantum Chemistry, 1998, 69:397-404.
9. Pan, W.; Lee, T.-S.; Yang, W., “Parallel implementation of divide-and-conquer semiempirical quantum chemistry calculations.”
Journal of Computational Chemistry, 1998, 19:1101-1109.
8. Lewis, J.P.; Carter, C.W.; Hermans, J.; Pan, W.; Lee, T.-S.; Yang, W., “Active species for the ground-state complex of cytidine deaminase: a linear-scaling quantum mechanical investigation.”
Journal of the American Chemical Society, 1998, 120:5407-5410.
7. York, D. M.; Lee, T.-S.; Yang, W., “Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods.”
Physical Review Letters, 1998, 80:5011-5014.
6. York, D. M.; Lee, T.-S.; Yang, W., “Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules.”
Chemical Physics Letters, 1996, 263:297-304.
5. York, D. M.; Lee, T.-S.; Yang, W., “Quantum mechanical study of aqueous polarization effects on biological macromolecules.”
Journal of the American Chemical Society, 1996, 118:10940-10941.
4. Lee, T.-S.; York, D. M.; Yang, W., “Linear-scaling semiempirical quantum calculations for macromolecules.”
Journal of Chemical Physics, 1996, 105:2744-2750.
3. Yang, W. and Lee, T.-S., “A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules.”
Journal of Chemical Physics, 1995, 103:5674-5678.
2. Lee, T.-S.; York, D. M.; Yang, W., “A new definition of atomic charges based on a variational principle for the electrostatic potential energy.”
Journal of Chemical Physics, 1995, 102:7549-7556.
1. Lee, T.-S.; Hwang, L.-P., “Influence of dipole-dipole cross-relaxation on spectal lineshapes of methyl protons in inversion-recovery experiments.”