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Computational biophysical chemistry,

Computer - aided drug design

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sun@ntnu.edu.tw

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°ê¥ß¥xÆW¤j¾Ç¤Æ¾Ç¨t(¾Ç¤h) B.S. in Chemistry, National Taiwan University, 1987

¬ü°ê»«¤iªk¥§¨È¤j¾Ç¤Æ¾Ç¬ã¨s©Ò(³Õ¤h) Ph.D. in Chemistry, Univ. of Pennsylvania, 1994

¬ü°ê¥[¦{¤j¾Çª÷¤s¤À®ÕÃIJz¤Æ¾Ç¨t(³Õ¤h«á¬ã¨s­û) Postdoc, Univ. of California, San Francisco, 1994~1996

°ê¥ß¥xÆW®v½d¤j¾Ç¤Æ¾Ç¨t °Æ±Ð±ÂAssociate Professor, National Taiwan Normal Univ., 1996~2000

°ê¥ß¥xÆW®v½d¤j¾Ç¤Æ¾Ç¨t ±Ð±ÂProfessor, National Taiwan Normal Univ., 2000- ¨´¤µ

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  1. ¹q¸£»²§UÃĪ«³]­p¡G¤À¤l°Ê¤O¾Ç¼ÒÀÀ¡BDocking¡B¨t²Î¥Íª«¾Ç¤èªk¡BQSAR¡C
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  3. ³J¥Õ½è¼ÒÀÀ¡GÐ`肽Áä§éÅ|¡A³J¥Õ½è»E¶°¡C

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Research Interests¡G

  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.

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A. Publications: ´Á¥Z½×¤å

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).

¡P        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 GSK3bƒn 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).

¡P        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).

¡P        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).

¡P        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)

¡P        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).

¡P        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).

¡P        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.

¡P        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.

¡P        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.

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Examination of reactions using QC methods

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

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

¡P        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).

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

¡P        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.

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B. Conference papers/¬ã°Q·|½×¤å

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.

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C. Others

§d«º¼_¡B§õ¨|»Ê¡Bµ{ÄR±ö¡B®]­^³Ç*, '³J¥Õ½è¤§¤À¤l¼ÒÀÀ("Protein simulation")', ª«²zÂù¤ë¥Z(Physics Bimonthly)¡]ÁܽZ(invited article)¡ATaipei, Taiwan, (¤Ü¤G¨÷¤T´Á¡^2000¦~6¤ë, June (2000).