1. Nanlan Huang and Jung-Hsin Lin*
    Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation
    Nucleic Acids Res. 43: 6772-6786 (2015).

  2. Pei-Lung Chen, Shyang-Rong Shih, Pei-Wen Wang, Ying-Chao Lin, Chen-Chung Chu, Jung-Hsin Lin, Szu-Chi Chen, Ching-Chung Chang, Tien-Shang Huang, Keh Sung Tsai, Fen-Yu Tseng, Chih-Yuan Wang, Jin-Ying Lu, Wei-Yih Chiu, Chien-Ching Chang, Yu-Hsuan Chen, Yuan-Tsong Chen, Cathy Shen-Jang Fann, Wei-Shiung Yang and Tien-Chun Chang
    Concurrent direct human leukocyte antigen (HLA) genotyping and genome-wide association study (GWAS) reveal major genetic determinants of anti-thyroid drug-induced agranulocytosis
    Nature Communications 6: 7633 (2015).

  3. Yu-Hsuan Chen and Jung-Hsin Lin*
    Prediction of functional types of ligands for G protein-coupled receptors with dynamically discriminable states embedded in low dimension.
    Lecture Notes in Computer Science 9044: 627-634 (2015).

  4. Pei-Teh Chang, Rahul Subhash Talekar, Fan-Lu Kung, Ting-Rong Chern, Chen-Wei Huang, Qing-qing Ye, Min-Yan Yang, Chao-Wu Yu, Shin-Yu Lai, Ravindra Ramesh Deore, Jung-Hsin Lin, Chien-Shu Chen, Grace Shiahuy Chen, Ji-Wang Chern
    A newly designed molecule J2326 for Alzheimer's disease disaggregates amyloid fibrils and induces neurite outgrowth
    Neuropharmacology 92: 146-157 (2015).

  5. Yi-Shan Lin, Jung-Hsin Lin, Chia-Chuan Chang, and Shoei-Sheng Lee
    Tetrahydropyran and Tetrahydrofuran Containing Diarylheptanoids from Hedychium coronarium Rhizomes
    J. Nat. Prod. 78: 181-187 (2015).

  6. Laurent Sabater, Pei-Ju Fang, Chi-Fon Chang, Aurore De Rache, Enora Prado, Jerôme Dejeu, Antonio Garofalo, Jung-Hsin Lin, Jean-Louii s Mergny, Eric Defrancq and Geneviève Pratviel
    Cobalt(III)porphyrin to target G-quadruplex DNA
    Dalton Transactions 44: 3701-3707 (2015).

  7. Jui-Chih Wang and Jung-Hsin Lin*
    Scoring Function for Fragment-Based Drug Discovery
    Chapter 9 of 'Methods in Molecular Biology', Anthony Klon (Editor), ISBN 978-1-4939-2486-8, Springer Verlag (2015).

  8. Nan-Lan Huang and Jung-Hsin Lin*
    Prediction of Binding Poses and Binding Affinities of Glycans and Their Binding Proteins Using a Robust Scoring Function for General Protein-Ligand Interactions
    In 'Proceedings of 2013 International Beilstein Symposium on Glyco-Bioinformaticsi --- Discovering the Subtleties of Sugars Martin G. Hicks and Carsten Kettner (Editors) (2014).

  9. Nan-Lan Huang and Jung-Hsin Lin*
    Drug-Induced Conformational Population Shifts in Topoisomerase-DNA Ternary Complexes
    Molecules 15: 7415-7428 (2014).

  10. Chiou-Tsun Tsai, Pei-Ming Yang, Ting-Rong Chern, Shu-Hui Chuang, Jung-Hsin Lin, Lars Klemm, Markus Müschen and Ching-Chow Chen
    AID downregulation is a novel function of the DNMT inhibitor 5-aza-deoxycytidine
    Oncotarget 5: 211-223 (2014).

  11. Jhih-Bin Chen , Ting-Rong Chern , Tzu-Tang Wei , Ching-Chow Chen , Jung-Hsin Lin*, and Jim-Min Fang*
    Design and synthesis of dual-action inhibitors targeting histone deacetylases and HMG-CoA reductase for cancer treatment
    J. Med. Chem. 56: 3645-3655 (2013).

  12. Jui-Chih Wang and Jung-Hsin Lin*
    Scoring functions for prediction of protein-ligand interactions
    Curr. Pharm. Des. 19: 2174-2182 (2013).

  13. Jung-Hsin Lin*
    Target prediction of small molecules with information of key molecular interactions
    Curr. Top. Med. Chem. 12: 1903-1910 (2012).

  14. Darby Tien-Hao Chang, Chao-Hsuan Ke, Jung-Hsin Lin, and Jung-Hsien Chiang
    AutoBind: Automatic extraction of protein-ligand binding affinity data from biological literature
    Bioinformatics 28: 2162-2168 (2012).

  15. Yi-Chao Lee, Ying-Chen Yang, Chuan-Lin Huang, Tsun-Yung Kuo, Jung-Hsin Lin, De-Ming Yang, Nai-Kuei Huang
    When cytokinin, a plant hormone, meets the adenosine A2A receptor: A new neuroprotectant and lead for treating neurodegenerative disorders?
    PLoS ONE 7: e38865 (2012).

  16. Jui-Chih Wang, Pei-Ying Chu, Chung-Ming Chen and Jung-Hsin Lin*
    idTarget: a web server for identifying proteins targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach
    Nucleic Acids Res. 40: W393-W399 (2012).

  17. Ravindra Ramesh Deore, Grace Shiahuy Chen, Pei-Teh Chang, Ting-Rong Chern, Shin-Yu Lai, Ming-Hsieh Chuang, Jung-Hsin Lin, Fan-Lu Kung, Chien-Shu Chen, Chun-Tang Chiou, Ji-Wang Chern
    Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide derivatives as HCV NS5B polymerase inhibitors
    ChemMedChem 7: 850-860 (2012).

  18. Jui-Chih Wang, Jung-Hsin Lin*, Chung-Ming Chen, Alex L. Perryman, Arthur J. Olson
    Robust scoring functions for protein-ligand interactions with quantum chemical charge models
    J. Chem. Inf. Model. 51: 2528-2537 (2011).

  19. Carmen Romera, Oriane Bombarde, Romaric Bonnet, Dennis Gomez, Pascal Dumy, Patrick Calsou, Jean-Fang Gwan, Jung-Hsin Lin, Eric Defrancq, Genevieve Pratviel
    Improvement of porphyrins for G-quadruplex DNA targeting
    Biochimie 93: 13010-1317 (2011).

  20. Nai-Kuei Huang,¥ Jung-Hsin Lin,¥ Jiun-Tsai Lin, Chia-I Lin, Eric Minwei Liu, Chun-Jung Lin, Wan-Ping Chen, Yuh-Chiang Shen, Hui-Mei Chen, Jhih-Bin Chen, Hsing-Lin Lai, Chieh-Wen Yang, Ming-Chang Chiang, Yu-Shuo Wu, Chen Chang, Jiang-Fan Chen, Jim-Min Fang, Yun-Lian Lin, Yijung Chern
    A new drug design targeting the adenosinergic system for Huntington's disease
    PLoS ONE 6: e20934 (2011).

  21. Jhih-Bin Chen, Eric Minwei Liu, Ting-Rong Chern, Chieh-Wen Yang, Chia-I Lin, Nai-Kuei Huang, Yun-Lian Lin, Yijuang Chern,Jung-Hsin Lin,* and Jim-Min Fang*
    Design and synthesis of novel dual-action compounds targeting adenosine A2A receptor and adenosine transporter for neuroprotection
    ChemMedChem. 6: 1390-1400 (2011).

  22. Jung-Hsin Lin*
    Accommodating protein flexibility for structure-based drug design
    Curr. Top. Med. Chem. 11: 171-178 (2011).

  23. Jui-Chih Wang and Jung-Hsin Lin*
    Robust regression analysis of protein-ligand binding free energy models: toward identification of druggable genomes
    Int. J. Syst. Syn. Biol. 1: 339-354 (2010).

  24. Darby Tien-Hao Chang, Jung-Hsin Lin, Chih-Hung Hsieh, and Yen-Jeng Oyang
    On the design of optimization algorithms for prediction of molecular interactions
    Int. J. Art. Intell. Tools 19: 267-280 (2010).

  25. Wei-Jan Huang, Chih-Chiang Huang, Ling-Wei Hsin, Yeun-Min Tsai, Chin-Ting Lin, Jung-Hsin Lin, and Shoei-Sheng Lee
    Improved enamine-type addition of dehydroaporphine using microwave irradiation
    Tetrahedron Lett. 51: 3062-3064 (2010).

  26. Jung-Hsin Lin, Jaakko Akola, and Robert O. Jones
    Structure and dynmics of large biological molecules: ATP-binding cassette (ABC) transporters
    In 'NIC Symposium 2010, Proceedings' G. Münster, D. Wolf, and M. Kreme (Editors), John von Neumann Institute for Computing, Jülich IAS Series Volume 3 ISBN 978-3-89336-606-4, pp. 84-91 (2010).

  27. Pei-Ming Yang, Jung-Hsin Lin, Wen-Yu Huang, Yi-Chu Lin, Shu-Hao Yeh, and Ching-Chow Chen
    Inhibition of histone deacetylase activity is a novel function of antifolate drug methotrexate
    Biochem. Biophys. Res. Comm. 391: 1396-1399 (2010).

  28. Yang-Shan Lin, Jung-Hsin Lin*, and Chien-Cheng Chang
    Molecular dynamics simulations of the rotary motor Fo under external electric fields across the membrane
    Biophys. J. 98: 1009-1017 (2010).

  29. Po-Hsien Lee, Kuei-Ling Kuo, Pei-Ying Chu, Eric M. Liu, and Jung-Hsin Lin*
    SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters
    Nucleic Acids Research 37: W559-W564 (2009).

  30. Yi-Chu Lin, Jung-Hsin Lin, Chia-Wei Chou, Yu-Fan Chang, Shu-Hao Yeh, and Ching-Chow Chen
    Statins increase p21 through inhibition of histone deacetylase activity and release of promoter-associated HDAC1/2
    Cancer Res. 68: 2375-2383 (2008) .

  31. Rommie E. Amaro, David D. L. Minh, Lily S. Cheng, William M. Lindstrom, Jr., Arthur J. Olson, Jung-Hsin Lin, Wilfred W. Li, and J. Andrew McCammon
    Remarkable loop flexibility in avian influenza N1 and its implications for antivirial drug design
    J. Am. Chem. Soc. 129: 7764-7765 (2007) .

  32. Shoei-Sheng Lee, Uppala Venkatesham, Chitneni Prasad Rao, Sio-Hong Lam, and Jung-Hsin Lin
    Preparation of secolycorines against acetylcholinesterase
    Bioorganic & Medicinal Chem. 15: 1034-1043 (2007) .

  33. Alexander L. Perryman, Jung-Hsin Lin, and J. Andrew McCammon
    Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design
    Chem. Biol. Drug Design 67: 336-345 (2006) .

  34. Darby Tien-Hao Chang, Yi-Zhong Weng, Jung-Hsin Lin, Ming-Jing Hwang, and Yen-Jen Oyang
    Promtemot: prediction of protein binding sites with automatically extracted geometrical templates
    Nucleic Acids Res. 34: W304-W309 (2006) .

  35. Alexander L. Perryman, Jung-Hsin Lin, and J. Andrew McCammon
    Restrained molecular dynamics of HIV-1 protease: Validating a new target for drug design.
    Biopolymers 82: 272-284 (2006) .

  36. Dominico Vigil, Jung-Hsin Lin, Christoph A. Sotriffer, Juniper K. Pennypacker, J. Andrew McCammon, and Susan S. Taylor
    A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP
    Prot. Sci. 15: 113-121 (2006) .

  37. Jennifer R. Giorgione, Jung-Hsin Lin, J. Andrew McCammon, and Alexandera C. Newton
    Increased membrane affinity of the C1 domain of protein kinase Cδ components for the lack of involvement of its C2 Domain in membrane recruitment.
    J. Biol. Chem. 281: 1660-1669 (2006) .

  38. Darby Tien-Hao Chang, Yen-Jen Oyang, and Jung-Hsin Lin*
    MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
    Nucleic Acids Res. 33: W233-W238 (2005) .

  39. Alexander L. Perryman, Jung-Hsin Lin, and J. Andrew McCammon
    HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new drug target site for drugs
    Prot. Sci. 13: 1108-1123 (2004) .

  40. Jung-Hsin Lin*, Alexander L. Perryman, Julie R. Schames, and J. Andrew McCammom
    The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    Biopolymers 68: 47-62 (2003) .

  41. Jung-Hsin Lin*, Nathan A. Baker, and J. Andrew McCammom
    Bridging implicit and explicit solvent approaches for membrane electrostatics
    Biophys. J. 83: 1374-1379 (2002).

  42. Jung-Hsin Lin*, Alexander L. Perryman, Julie R. Schames, and J. Andrew McCammom
    Computational drug design acommodating receptor flexibility: The relaxed complex scheme
    J. Am. Chem. Soc. 124: 5632-5633 (2002).

  43. Jung-Hsin Lin.
    Structures, dynamics, and energetics of protein membrane interactions: Molecular dynamics studies.
    Ph.D. Thesis (submitted September 29, accepted December 10, 1999, disputed January 3, 2000).

  44. Jung-Hsin Lin and Artur Baumgaertner.
    Stability of a melittin pore in a lipid bilayer : a molecular dynamics study.
    Biophys. J. 78: 1714-1724 (2000).

  45. Jung-Hsin Lin and Artur Baumgaertner.
    Molecular dynamics simulations of hydrophobic and amphiphatic proteins interacting with a lipid bilayer membrane.
    Comput. Theor. Poly. Sci. 10:1-2 97-102 (2000).

  46. Jung-Hsin Lin and Artur Baumgaertner.
    Adsorption of melittin to a lipid bilayer : a molecular dynamics study.
    J. Mol. Liquids 84:1 89-98 (2000) .

  47. Jung-Hsin Lin and Artur Baumgaertner.
    A Combined Monte Carlo/molecular dynamics simulation of a hypothetical melittin pore.
    In Molecular Dynamics on Parallel Computers, p.338 edited by R. Esser, P. Grassberger and J. Grotendorst World Scientific Publishing Co. Pte. Ltd., (2000) .

  48. Jung-Hsin Lin and Artur Baumgaertner.
    Molecular dynamics simulation of melittin at the POPC membrane/water interface.
    In Molecular Dynamics on Parallel Computers, p. 336 edited by R. Esser, P. Grassberger and J. Grotendorst World Scientific Publishing Co. Pte. Ltd., (2000) .

  49. Jung-Hsin Lin and Artur Baumgaertner.
    Computersimulation zum Transportprozess eines Proteins.
    Zeitschrift Nachrichten aus Chemie 7/8, Zeitschrift der GDCh, S.734, (1998) .

  50. Jung-Hsin Lin, Nina von Westernhagen, and Artur Baumgaertner.
    Computersimulation eines Ionenkanals.
    Bilder Wissenschaft,11/1998.