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Computational biophysical chemistry,

Computer - aided drug design

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國立台灣大學化學系(學士) B.S. in Chemistry, National Taiwan University, 1987

美國賓夕法尼亞大學化學研究所(博士) Ph.D. in Chemistry, Univ. of Pennsylvania, 1994

美國加州大學舊金山分校藥理化學系(博士後研究員) Postdoc, Univ. of California, San Francisco, 1994~1996

國立台灣師範大學化學系 副教授Associate Professor, National Taiwan Normal Univ., 1996~2000

國立台灣師範大學化學系 教授Professor, National Taiwan Normal Univ., 2000- 迄今



  1. 電腦輔助藥物設計:分子動力學模擬、Docking、系統生物學方法QSAR
  2. 癌症藥物、神經退化性疾病藥物研發。
  3. 蛋白質模擬:胜肽鍵折疊,蛋白質聚集。


Research Interests

  1. Computer - aided drug design : molecular dynamics simulation, Docking, Systems biology, QSAR methods,.
  2. Diseases targeted : cancer, neurodegenerative diseases.
  3. Protein simulation : peptide folding, protein aggregation.



A. Publications: 期刊論文

Biophysical chemistry

  • Chih-Hsin Lin, Yu-Shao Hsieh, Yih-Ru Wu, Chia-Jen Hsu, Hsuan-Chiang Chen, Hsiu Mei Hsieh-Li, Ming-Tsan Su, Ying-Chieh Sun*, Guan-Chiun Lee*, Guey-Jen Lee-Chen*, "Identifying GSK-3<beta> kinase inhibitors of Alzheimer's disease: Virtual screening, enzyme, and cell assays", European Journal of Pharmaceutical Sciences (accepted 2016)
  • Ying-Chieh Sun, Wen-Chi Hsu, Chia-Jen Hsu, Chia-Ming Chang, Kai-Hsiang Cheng, "Investigation of differences in the Binding Affinity Differences in Ligands with un-Tagged and Tagged p38 Kinase Using Thermodynamic Integration MD Simulation" J. Mol. Model., 21, 283 (2015).
  • Hsing-Chou Lee; Wen-Chi Hsu; An-Lun Liu; Chia-Jen Hsu; Ying-Chieh Sun, “Using Thermodynamic Integration MD Simulation to Compute Relative Protein-Ligand Binding Free Energy of a GSK3ß Kinase Inhibitor and its Analogs”, J. Mol. Graphics & Model. 51,37-49, (2014)
  • Kuan-Wei Wu, Po-Chin Chen, Jun Wang, Ying-Chieh Sun, "Computation of Relative Binding Free Energy for an Inhibitor and its Analogs Binding with Erk Kinase Using Thermodynamic Integration MD Simulation", J. Comput. Aided Mol. Des. 26, 1159-1169 (2012). DOI 10.1007/s10822-012-9606-6
  • Xu-Nan Tang, Cheng-Wei Lo, Yu-Chung Chuang, Chao-Tung Chen, Ying-Chieh Sun, Yi-Ren Hong, and Chia-Ning Yang, Prediction of the binding mode between GSK3b and a peptide derived from GSKIP using molecular dynamics simulation”, Biopolymers, (accepted).

·        Jia-Yang Chen, Sin-Ming Huang, Yen-An Tang, Hsueh-Fen Juan, Li-Wha Wu, Ying-Chieh Sun, Szu-Chi Wang, Kuan-Wei Wu, Gopula Balraj, Tzu-Tin Chang, Wen-Shan Li, Hung-Chi Cheng, and Yi-Ching Wang, "A novel sialyltransferase inhibitor suppresses FAK/paxillin and angiogenesis signaling and cancer metastasis”, Cancer Research, 71, 473-483 (2011).

  • Ying-Chieh Sun, “Examination of Effects of GSK3bn Phosphorylation, b-catenin Phosphorylation, and b-catenin Degradation in Kinetics of Wnt Signaling Pathway Using Computational Method” Theore. Biol. Med. Modelling, 6: 13 (2009).
  • InLin Chiu and Ying-Chieh Sun, “Calculation of Binding Affinity for Colchicine Analogues Binding with Tubulin Using MD/MM-PBSA Method” (in preparation)
  • Cheng-Chang Hsu, Shih-Hong Wang, Hsing-Pang Hsieh, and Ying-Chieh Sun “Comparative Molecular Field Analysis of Anti-tubulin Agents with Indole Ring Binding at the Colchicine Binding Site”, J. Theore. Comput. Chem. 9, 279-291 (2010).
  • Shu-Ping Lin, Kun-Chang Tseng, Ming-Chou Lin, Chii-Dong Chen, Chia-Chang Tsai, Shu-Han Yu, Ying-Chieh Sun, Tsung-Wu Lin, Chien-Yuan Pan, and Yit-Tsong Chen, “A Reversible Surface Functionalized Nanowire Transistor to Study Protein-Protein Interactions" Nano Today, 4, 235-243 (2009).

·        Wen-Hung Wang, Yi-Ching Wang, and Ying-Chieh Sun, ‘A 3D-QSAR study of Celebrex-based PDK1 Inhibitors Using CoMFA Method’ J. Chin. Chem. Soc. 56, 59-64 (2009).

·        Yi-Hung Tan, Kung-Hsueh Lee, Topp Lin , Ying-Chieh Sun , Hsueh-Fen Juan, Yi-Ching Wang , ‘Cytotoxicity and Proteomics Analyses of OSU03013 in Lung Cancer’, Clinical Cancer Research, 14, 1823-1830 (2008).

·        C.C. Chen, Chung-Cheng Wei , Ying-chieh Sun and Chi-Ming Chen , ''Packing of Transmembrane Helices in Bacteriorhodopsin Folding: Structure and Thermodynamics’, Journal of Structural Biology, 162, 237-247 (2008)

·        Wei-Zhou Wang, Topp Lin , and Ying-Chieh Sun , ‘Examination of the Folding of a Short Alanine-Based Helical Peptide with Salt Bridges Using Molecular Dynamics Simulation’ J. Phys. Chem. B, 111, 3508-3514, (2007).

·        Yi-Len Tsai, Hwung-Wen Chen , Topp Lin , WeiZhou Wang , and Ying-Chieh Sun ‘Molecular Dynamics Simulation of Folding of a Short Helical Toxin Peptide’ J. Theore. Comput. Chem. 6, 213-221 (2007).

·        Chung-Cheng Wei, Ming-Hsun Ho, Wen-Hung Wang, and Ying-Chieh Sun ‘Molecular Dynamics Simulation of Folding of a Short Helical Peptide with Many Charged Residues’, J. Phys. Chem. B, 109, 19980-19986, (2005). SCI.

·        Ying-Chieh Sun, Shu-Fen Yang, I-Lun Hwang,and Tzu-Hsien Wu, 1999 `A 500 ps Molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: correlation with NMR and X-ray crystallography data‘  J. Comput. Chem., 20, 546-562. SCI.

·        Ying-Chieh Sun, David L. Veenstra, and Peter A.Kollman,1996”Free energy calculations of the mutation of the ILE96->ALA in barnase: contributions to the difference in stability`` Protein  Engineering,9.273-281. SCI.


Examination of reactions using QC methods

·        Chai Ling Fan, Wei-Der Lee, Nai-Wei Teng, Ying-Chieh Sun and Kwunmin Chen, ' Asymmetric Epoxidation of Camphor N-Enoylpyrazolidinones with Methyl(trifluoromethyl)dioxirane and Urea Hydrogen Peroxide Complex: Reversal of Stereoselectivity ' J. Org. Chem. 68, 9816, (2003). SCI.

·        Ying-Chieh Sun, I-Ting Wang, Thanh Lam Nguyen, Hsiu-Feng Lu, Xueming Yang, and Alexander M. Mebel ‘A Combined Quantum Chemistry and RRKM Calculation Predicts the O(1D) + C2H6 Reaction Can Produce Water Molecule in Collision-free Crossed Molecular Beam Environment", J. Phys. Chem. A 107, 6986-6994 (2003). SCI.

·        Pei-Fang Wu, I-Ting Wang, Hsiu-Feng Lu, Ching-Fa Yao, and Ying-Chieh Sun, ‘A Theoretical Study of Face Selectivity in the Michael Addition of a Grignard Reagent with 5-substituted-2-dicyanomethyleneadamantanes’, J. Chin. Chem. Soc. (special issue) 50, 545 (2003). SCI.

·        Hsiu-Feng Lu and Ying-Chieh Sun, ‘Calculated Energies of Adsorption of Non-hydrocarbon Species on Diamond H/C(111) Surface and the Abstraction Energies of these Species Abstracted by Hydrogen Atoms Using ab initio Calculation’ Diamond and Related Materials, 11, 1560 (2002) . SCI.

·        Man-kit Leung, Ashis B. Mandal, Chih-Chieh Wang, Gene-Hsiang Lee, Shie-Ming Peng, Hsing-Ling Cheng, Guor-Rong Her, Ito Chao,, Hsiu-feng Lu, Ying-Chieh Sun, Mei-Ying Shiao, and Pi-Tai Chou, ‘Self-complementarity of oligo-a-aminopyridines: a new class of hydrogen-bonded ladders’, J. Am. Chem. Soc., 124, 4287 (2002), . SCI.

·        Hsiu-Feng Lu and Ying-Chieh Sun, ‘Calculation of Hydrogen Abstraction Reaction on Hydrogen-covered H/C(111) Diamond Surface Abstracted by Non-Hydrocarbon Species’, Surf. Sci. 494 L787-L792 (2001). SCI.


Vibrational energy relaxation MD simulation, path integral MC simulation, first-principle quantum-mechanical MD simulation

·        Jeng-Han Wang, M. C. Lin, Ying-Chieh Sun, ' Reactions of Hydrazoic Acid on TiO2 Nanoparticles: An Experimental and Computational Study'. J. Phys.  Chem. B, 109, 5133-5142 (2005).

·        Ming-Hsun Ho and Ying-Chieh Sun, ‘Molecular Dynamics Simulation of Hydrogen-covered Si(100):H-2x1 surface: Calculation of Vibrational Energy Relaxation Rates of Hydrogen Stretching Modes’, Surf. Sci., 516, L540-L546 (2002). SCI.

·        Sho-Ching Hong, Ming-Shun Ho, Hsiu-Feng Lu, and Ying-Chieh Sun, 2000, `Calculated lifetime of the first (v=1) Ge-H stretching excited state on hydrogen-covered H/Ge(111) germanium surface’, J. Chin. Chem. Soc., 47, 881-886. SCI.

·        Ying-Chieh Sun, Hsiu-Feng Lu, and Ming-Shun Ho, 2000,`Molecular dynamics simulation of hydrogen isotope-terminated silicon (111) and (110) surfaces: calculation of vibrational energy relaxation rates of hydrogen isotope stretching modes’, Chem. Phys. Lett., 318, 7-14. SCI.

·        Hsiu-Feng Lu, Ming-Shun Ho, Sho-Ching Hong, Ai-Hsin Liu, Pei-Fang Wu, and Ying-Chieh Sun, 1998 ‘Determination of vibrational energy relaxation rates of C-H,D,T stretching modes on hydrogen, deuterium, and tritium-terminated H,D,T/C(111) and H,D,T/C(110) surfaces using molecular dynamics simulation: thermal effect’ J. Chem. Phys., 109,6898-6904. SCI.

·        Ying-Chieh Sun and Jiunn-Ming Chen, 1997 ‘ Calculations of vibrational energy relaxation rates of C-H,D,T stretching modes on hydrogen, deuterium, and tritium-terminated H,D,T/C(111)lxl surface’ J. Phys. Chem.,101, 7082-7086. SCI.

·        Ying-Chieh Sun, Huadong Gai and Gregory A.Voth,1995”Vibrational energy relaxation dynamics of Si-H stretching modes on stepped H/Si(lll)lxl surface”Chem.Phys.,200,357-368, SCI.

·        Ying-Chieh Sun, Huadong Gai and Gregory A.Voth,1994”Vibrational energy relaxation dynamics of C-H stretching modes on the hydrogen-terminated H/C(111)lxl surface”J. Chem. Phys.,100,3247-3251, SCI.

·        Ying-Chieh Sun and Gregory A. Voth, 1993 ”Path integral calculation of hydrogen diffusion rates on metal surfaces”J. Chem. Phys., 98, 7451-7458, SCI.


B. Conference papers/研討會論文

Jeng-Chiy Yian, Yu-Ming Lee, Tzu-Hsien Wu, and Ying-chieh Sun*, `Thermal molecular dynamics simulations of cardiotoxin III from Taiwan cobra venom in solution, an invited article contributed to the Third Tohwa University International Conference on Statistical Physics, Am. Inst. Phys. Conference Proceedings, invited speaker, Tohwa University, Japan, Nov. 1999.


C. Others

吳姿嫻、李育銘、程麗梅、孫英傑*, '蛋白質之分子模擬("Protein simulation")', 物理雙月刊(Physics Bimonthly)(邀稿(invited article)Taipei, Taiwan, (廿二卷三期)20006, June (2000).