CURRICULUM VITAE

     

    Yuno Lee

  • Hobby : Listening Music, Web Surfing.
  • Expertise: Molecular Modeling (molecular docking, protein-protein docking, molecular dynamics, membrane simulation, QM/MM, free energy calculation, NMR refinement, protein engineering), Computer-aided Drug Design (3D-QSAR, pharmacophore model generations, and virtual screening), Computer Programming
  • Affiliation: Korea Institute for Advanced Study (KIAS), Computational Sciences, Theoretical and Computational Biophysics Lab (Prof. Changbong Hyeon).
  • Current works: Writing papers based on results obtained from many projects.
  • more photos: portrait2009   portrait2014

 

PUBLICATIONS

Research Papers

    2014

  • 40.
  • 39. “Generation of chickenized catalytic anti-nucleic acid antibody by complementarity-determining region grafting Molecular Immunology” Molecular Immunology in press (IF2013: 3.003)
     
  • 38. S. Ghatge, A. Telke, T. Waghmode, Y. Lee, K. W. Lee, D-B. Oh, H-D. Shin, and S-W. Kim, “Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose” Applied Microbiology and Biotechnology (2014.10 online) [ PDF ] (IF2013: 3.811).
     
  • 37. Y. Lee*, J-j Lee*, S. Kim*, S-C. Lee, J. Han, K. Park, H. J. Kim, H-K. Cheong, D. Kim, H-S. Kim, K. W. Lee, “Dissecting the critical factors for thermodynamic stability of modular proteins using molecular modeling approach.” PLoS One (2014.05) [ PDF ] (IF2012: 3.73).
     
  • 36. M. Son*, W. Y. Bang*, C. Park, Y. Lee, S. G. Kwon, S. W. Kim, C. W. Kim, K. W. Lee, “Functional Mechanism of C-terminal Tail in the Enzymatic Role of Porcine Testicular Carbonyl Reductase: a combined experiment and molecular dynamics simulation study of the C-terminal tail in the enzymatic role of PTCR” PLoS One 9(3), e90712 (2014.03) [ PDF ] (IF2012: 3.73).
     
  • 35. Y. Lee*, S. Kim*, Jun Young Kim, M. Arooj, S. Kim, S. Hwang, B-W. Kim, K. H. Park, K. W. Lee “Binding mode analyses and pharmacophore model development for Stilbene Derivatives, a Novel and Competitive Class of α-Glucosidase Inhibitors.” PLoS One 9(1), e85827 (2014.01) [ PDF ] (IF2012: 3.73).
     
  • 34. J. Chen, W. Y. Bang, Y. Lee, S. Kim, K. W. Lee, S. W. Kim, Y. S. Son, D. W. Kim, S. Akhter, J. D. Bahk, “AtObgC-AtRSH1 interaction may play a vital role in stress response signal transduction in Arabidopsis” Plant Physiology and Biochemistry 74, 176-184 (2014.01) [ HTML ] (IF2012: 2.775).
     
  • 2013

  • 33. Y-s. Sohn, C. Park, Y. Lee, S. Kim, S. Thangapandian, Y. Kim, H-H. Kim, K. W. Lee, “Multi-Conformation Dynamic Pharmacophore Modeling of the Peroxisome Proliferator-Activated Receptor γ for the Discovery of Novel Agonists.” Journal of Molecular Graphics and Modeling 46, 1-9 (2013.11) [ PDF ] (IF2012: 2.325).
     
  • 32. Y. J. Jung*, Y. H. Chi*, H. B. Chae, M. R. Shin, E. S. Lee, J-Y. Cha, S. K. Paeng, Y. Lee, J. H. Park, W. Y. Kim, C. H. Kang, K. O. Lee, K. W. Lee, D-J. Yun, S. Y. Lee, “Analysis of Arabidopsis thioredoxin-h isotypes identifies discrete domains that confer specific structural and functional properties” (Y. Lee performed all the molecular modeling study) Biochemical Journal 456, 13-24 (2013.11) [ HTML ] (IF2012: 4.654).
     
  • 31. S. Lee, Y. Lee, James M. Briggs, K. W. Lee, "Pharmacophore Models of Paclitaxel- and Epothilone-Based Microtubule Stabilizing Agents." Bulletin of the Korean Chemical Society 34(7), 1972-1984 (2013.07) [ PDF ] (IF2012: 0.982).
     
  • 30. M. Arooj, S. Kim, S. Sakkiah, G. Cao, Y. Lee, K. W. Lee, "Molecular Modeling Study for Inhibition Mechanism of Human Chymase and Its Application in Inhibitor Design." PLoS One 8(4), e62740 (2013.04) [ PDF ] (IF2012: 3.73).
     
  • 29. S. Kim*, Y. Lee*, H-M. Tak, H-J. Park, Y-S. Sohn, S. Hwang, J. Han, D. Kang, K. W. Lee, "Identification of blocker binding site in mouse TRESK by molecular modeling and mutational studies." BBA-Biomembranes 1828(3), 1131-1142 (2013.03) [ PDF ] (IF2011: 3.99).
     
  • 28. M. chandrasekaran, S. Sakkiah, Y. Lee, J. V. Narayanan, K. W. Lee, "Discovery of potent inhibitors for interleukin-2-inducible T-cell kinase: structure-based virtual screening and molecular dynamics simulation approaches." Journal of Molecular Modeling 19(2), 715-726 (2013.02) [ PDF ] (IF2011: 1.797).
     
  • 2012

  • 27. S. Thangapandian, S. Sohn, Y. Lee, V. Arulalapperumal, K. W. Lee, "Molecular Modeling Study on Tunnel Behavior in Different Histone Deacetylase Isoforms." PLoS One 7(11), e49327 (2012.11) [ PDF ] (IF2011: 4.092).
     
  • 26. Y. Lee*, S. Kim*, P. Lazar, J. Moon, S. Hwang, S. Thangapandian, Y. Shon, K. O. Lee, S. Y. Lee, K. W. Lee, "Comparative Molecular Modeling Study of Arabidopsis NADPH-Dependent Thioredoxin Reductase and Its Hybrid Protein." PLoS One 7(9), e46279 (2012.09) [ PDF ] (IF2011: 4.092).
     
  • 25. W. Jung, S. Kwon, M. Son, E. Cho, Y. Lee, J. Kim, B. Kim, D. Park, J. Hwang, T. Kim, H. Park, B. Park, J. Choi, K. Cho, K. Chung, Y. Song, I. Kim, S. Jin, D. Kim, S. Lee, K. W. Lee, W. Y. Bang, C. W. Kim, "RNA-Seq Approach for Genetic Improvement of Meat Quality in Pig and Evolutionary Insight into the Substrate Specificity of Animal Carbonyl Reductases." PLoS One 7(9), e42198 (2012.09) [ PDF ] (IF2011: 4.092).
     
  • 24. B. Lee, H. Lim, S. Kim, H. Youn, Y. Lee, Y. Kim, S. Eom, K. W. Lee, C. Park, "Localization of a Site of Action for Benzofuroindole-induced Potentiation of BK Channels." Molecular Pharmacology 82(2), 143-155 (2012.08) [ PDF ] (IF2011: 4.883).
     
  • 23. S. Sakkiah, M. Chandrasekaran, Y. Lee, S. Kim, K. W. Lee, "Molecular Modeling Study for Conformational Changes of Sirtuin2 due to Substrate and Inhibitor Binding." Journal of Biomolecular Structure & Dynamics 30(3), 235-254 (2012.07) [ PDF ] (IF2010: 4.986).
     
  • 22. V. Arulalapperumal, S. Sakkiah, S. Thangapandian, Y. Lee, C. Meganathan, S. Hwang, K. W. Lee, "Ligand Based Pharmacophore Identification and Molecular Docking Studies for Grb2 Inhibitors." Bulletin of the Korean Chemical Society 33(5), 1707-1714 (2012.05) [ PDF ] (IF2011: 0.906).
     
  • 2011

  • 21. Y. S. Lee, K. S. Ryu, Y. Lee, S. Kim, K. W. Lee, H. S. Won, "Oxidation-Induced Conformational Change of a Prokaryotic Molecular Chaperone, Hsp33, Monitored by Selective Isotope Labeling." Journal of the Korean Magnetic Resonance Society 15(1), 137-145 (2011.12) [PDF] (KCI).
     
  • 20. S. Thangapandian, S. John, Y. Lee, S. Kim, K. W. Lee, "Dynamic Structure-Based Pharmacophore Model Development: A New and Effective Addition in the Histone Deacetylase 8 (HDAC8) Inhibitor Discovery." International Journal of Molecular Sciences 12(12), 9440-9462 (2011.12) [ PDF] (IF2010: 2.279).
     
  • 19. S. Hwang, S. Thangapandian, Y. Lee, S. Sakkiah, S. John , K. W. Lee, "Discovery and Evaluation of Potential Sonic Hedgehog Signaling Pathway Inhibitors using Pharmacophore Modeling and Molecular Dynamics Simulations." Journal of Bioinformatics and Computational Biology 9(Suppl 1), 15-35 (2011.12) [ PDF ] (SCIE).
     
  • 18. S. Kim, Y. Lee, P. Lazar, M. Son, A. Baek, S. Thangapandian, N. Y. Jeong, Y. H. You, K. W. Lee, "Binding Conformation Prediction between Human Acetylcholinesterase and Cytochrome c using Molecular Modeling Methods." Journal of Molecular Graphics and Modeling 29(8), 996-1005 (2011.08) [ PDF ] [ Selected as Top 25 Hottest Articles ] (IF2010: 2.038).
     
  • 17. Y. Sohn, Y. Lee, C. Park, S. Hwang, S. Kim, A. Baek, M. Son, J. Suh, H. Kim, K.W. Lee, "Pharmacophore Identification for Peroxisome Proliferater-Activated Receptor gamma Agonists." Bull. Korean Chem. Soc. (in press)[ PDF ] (IF2009: 0.936).
     
  • 2010

  • 14. P. Lazar, Y. Lee, S. Kim, K. W. Lee, "Computational approach to ensure the stability of the favorable ATP binding site in E.coli Hfq." Journal of Molecular Graphics and Modeling 29(4), 573-580 (2010.12) [ PDF ] (IF2009: 2.169).
     
  • 13. J. Y. Kim, J. W. Lee, Y. S. Kim, Y. Lee, Y. B. Ryu, S. Kim, H. W. Ryu, M. J. Curtis-Long, K. W. Lee, W. S. Lee, K. H. Park, "A Novel Competitive Class of α-Glucosidase Inhibitors: (E)-1-Phenyl-3-(4-Stryrylphenyl)Urea Derivatives." ChemBioChem 11(15), 2125-2131 (2010.10) [ PDF ] (IF2009: 3.824).
     
  • 14. Y. Lee, W. Y. Bang, S. Kim, P. Lazar, C. W. Kim, J. D. Bahk, K. W. Lee, "Molecular Modeling Study for Interaction between Bacillus subtilis Obg and Nucleotides." PLoS ONE 5(9), e12597 (2010.09) [ PDF ] (IF2009: 4.351)
     
  • 13. P. Lazar, Y. Lee, S. Kim, M. Chandrasekaran, K. W. Lee, "Molecular Dynamics Simulation Study for Ionic Strength Dependence of RNA-host factor Interaction in Staphylococcus aureus Hfq" Bull. Korean Chem. Soc. 31(6), 1519-1526 (2010) [ PDF ] (IF: 1.257)
     
  • 12. H.-S. Eum*, Y. Lee*, S. Kim, M. Son, K. W. Lee, S. W. Ko, S. Kim, S. Y. Yun, W.-K. Lee and H.-J. Ha, "Synthesis of Substituted Imidazolidin-2-ones as Aminoacyl-tRNA Synthase Inhibitors." Bull. Korean Chem. Soc. 31(3), 611-614 (2010) (*Co-First Authors) [ PDF ] (IF: 1.257)
     
  • 11. N. Bharatham, K. Bharatham, Y. Lee, S. Kim, P. Lazar, A. Baek, C. Park, H.-S. Eum, H.-J. Ha, S.-Y. Yun and K. W. Lee, "Molecular Docking Study of Aminoacyl-tRNA Synthetases (aaRSs) with Ligand Molecules from Four Different Scaffolds." Bull. Korean Chem. Soc. 31(3), 606-610 (2010) [ PDF ] (IF: 1.257)
     
  • 10. S. Thangapandian, N. Krishnamoorthy, S. John, S. Sakkiah, P. Lazar, Y. Lee and K. W. Lee, "Pharmacophore Modeling, Virtual Screening and Molecular Docking Studies for Identification of New Inverse Agonists of Human Histamine H1 Receptor" Bull. Korean Chem. Soc. 31(1), 52-58 (2010) [ PDF ] (IF: 1.257)
     
  • 9. N. Krishnamoorthy, P. Gajendrarao, Y. Lee, K. W. Lee, "Probing Possible Egress Channels for Multiple Ligands in Human CYP3A4: A Molecular Modeling Study." Journal of Molecular Modeling (2010) [ PDF ] (IF: 2.018)
     
  • 2009

  • 8. P. Lazar, S. Kim, Y. Lee, K. W. Lee, "Molecular Modeling Study on the Effect of Residues Distant from the Nucleotide Binding Portion on RNA Binding in Staphylococcus aureus Hfq." Journal of Molecular Graphics and Modeling (2009.10) [ PDF ] (IF: 2.347)
     
  • 7. Woo Young Bang, Akira Hata, In Sil Jeong, Tetsuya Umeda, Takayuki Masuda, Ji Chen, Ishizaki Yoko, I Nengah Suwastika, Dae Won Kim, Chak Han Im, Byung Hyun Lee, Yuno Lee, Keun Woo Lee, Takashi Shiina and Jeong Dong Bahk, "AtObgC, a plant ortholog of bacterial Obg, is a chloroplast-targeting GTPase essential for early embryogenesis." Plant Molecular Biology DOI: 10.1007/s11103-009-9529-3 (2009.07) [ PDF | WWW ] (IF: 3.541)
     
  • 6. N. Bharatham, K. Bharatham, Y. Lee, K. W. Lee, "Molecular Dynamics Simulation Study of Valyl-tRNA Synthetase with its Pre- and Post-transfer Editing Substrates." Biophysical Chemistry 143 (1-2) 34-43 (2009.07) [ PDF ] (IF: 1.913)
     
  • 5. S. Sakkiah, N. Krishnamoorthy, P. Gajendrarao, S. Thangapandian, Y. Lee, S. Kim, J.-K. Suh, H.-H. Kim, K. W. Lee, "Pharmacophore Mapping and Virtual Screening for SIRT1 Activators." Bull. Korean Chem. Soc. 30(5) 1152-1156 (2009.05). [ PDF ] (IF: 1.257)
     
  • 4. Y. Lee, W. Bang, S. Kim, P. Lazar, J. D. Bahk, K. W. Lee, "Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study."Interdisciplinary Bio Central DOI:10.4051/ibc.2009.1.0003 (2009.03) [ PDF ] [ WWW ] (IF: Not SCI)
     
  • 2007

  • 3. Y. Lee, N. Bharatham, K. Bharatham, K. W. Lee, "Adenosine Kinase Inhibitor Design Based on Pharmacophore Modeling." Bull. Korean Chem. Soc. 28(4) 561-566 (2007.04). [ PDF ] (IF: 1.257)
     
  • 2. 김병우, 이근우, 김효선, 노승희, 박준수, 이윤호, 전진태, 권은정, 김철욱, 이정규, "TIGR Gene Indices를 이용한 돼지 cDNA Chip 제작용 후보유전자 염기서열 확보 방안" Bioinformatics and Biosystems 1(3) 174-180 (2006.09) [ PDF ]
     
  • 1. 김병우, 이근우, 김효선, 노승희, 이윤호, 김시동, 전진태, 이지웅, 조용민, 정일정, 이정규, "생물정보시스템을 이용한 Local Animal BLAST Search System 구축." Bioinformatics and Biosystems 1(2) 99-102 (2006.06) [ PDF
     

 

Poster Presentations

    2014 

  • 59. Y. Lee, S. Kim, K. W. Lee, “Molecular modeling study of AtTrx-hs for predicting their thermo-stability, chaperone function, and oligomerization” in 58th Annual Meeting of The Biophysical Society, Moscone Center, San Francisco, California, USA, Feb. 15-19, 2014.
     
  • 58. S. Kim, Y. Lee, K. W. Lee, “Effect of F156 and F364 residues in Mouse TRESK for K+ Channel Blockers using Molecular Dynamics Simulation with Lipid Bilayer” in 58th Annual Meeting of The Biophysical Society, Moscone Center, San Francisco, California, USA, Feb. 15-19, 2014.
     
  • 2013 

  • 57. P. G. Heo, Y. Lee, S. Kim, H. S. Lee, K. W. Lee, “VASOPRESSIN V2 Receptor Inhibitor Design using 3D QSAR Pharmacophore Modeling” in 2013 Fall Conference of The Korean Society of Medical Informatics and Korean Society for Bioinformatics and Systems Biology, Busan Youth Hostel ARPINA, Busan, Korea, Nov. 11-13, 2013.
     
  • 56. V. Arulalapperumal, Y. Lee, M. Arooj, C. Park, A. Baek, G. Cao, K. W. Lee, “Prediction of Functionally Important Genes for Target Identification of Lung Cancer Disease from TGF- β Induced Epithelial Mesenchymal Transition (EMT) Model Cells” in 2013 Fall Conference of The Korean Society of Medical Informatics and Korean Society for Bioinformatics and Systems Biology, Busan Youth Hostel ARPINA, Busan, Korea, Nov. 11-13, 2013.
     
  • 55. H. S. Lee, Y. Lee, S. Kim, P. G. Heo, K. W. Lee, “C5a Anphylatoxin Receptor Inhibitor Design using 3D QSAR Pharmacophore Modeling” in 2013 Fall Conference of The Korean Society of Medical Informatics and Korean Society for Bioinformatics and Systems Biology, Busan Youth Hostel ARPINA, Busan, Korea, Nov. 11-13, 2013.
     
  • 54. Y. Lee, S. Kim, K. W. Lee, "Modeling Approach for Consensus Design of VLR Repeat Proteins: Relationship between Thermostability and Repeat Module Number” in 2013 Fall Conference of The Korean Society of Medical Informatics and Korean Society for Bioinformatics and Systems Biology, Busan Youth Hostel ARPINA, Busan, Korea, Nov. 11-13, 2013. (3 min. oral presentation competition) [Best Poster Award (1st winner)]
     
  • 53. Y. Lee, S. Kim, K. W. Lee, "Binding Mode Analyses and Pharmacophore Model Development for Stilbene Derivatives as a Novel and competitive Class of α-Glucosidase Inhibitors" in the DrugDesign2012, in the 7th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (CMTPI-2013), Grand Hilton Seoul, Seoul, Korea, Oct. 8-12, 2013. [Oral presentation]
     
  • 52. C. Park, S. Thangapandian, Y. Lee, M. Son, S. John, Y. Sohn, K. W. Lee, "Molecular Dynamic Simulation and Receptor-based Pharmacophore Modeling on Human Renin for Discovery of Novel Inhibitors." International Conference on Computational Modeling, Analysis and Simulation 2013, Geroldswil Swiss Quality Hotel, Geroldswil Zurich, Switzerland, Jan. 14-15, 2013.
     
  • 2012 

  • 51. S. Kim, Y. Lee, K. W. Lee, "Identification of Blocker Binding Site in Mouse TRESK Potassium Channel by Molecular Modeling Study." in the DrugDesign2012, 1st International Conference and Exhibition, St Hilda's College, Oxford, UK, Sep. 26-28, 2012.
     
  • 50. Y. Lee, S. Kim, K. W. Lee, "Combined Approach of Molecular Docking and Molecular Dynamics Simulations for Stibene Derivatives as a Novel and Competitive Class of α-Glucosidase Inhibitors." in the DrugDesign2012, 1st International Conference and Exhibition, St Hilda's College, Oxford, UK, Sep. 26-28, 2012.
     
  • 49. S. Kim, Y. Lee, K. W. Lee, "Identification of Blocker Binding Site and Critical Chemical Features for TREK-2 Potassium Channel by Molecular Docking Simulation and Structure-based Pharmacophore Modeling." in the DrugDesign2012, 1st International Conference and Exhibition, St Hilda's College, Oxford, UK, Sep. 26-28, 2012.
     
  • 2011  

  • 48. Y. Lee, S. Kim, K. W. Lee, "Molecular Dynamics Simulation Study for Understanding of Electron Transfer Mechanism in Escherichia coli Thioredoxin Reductase" in the 22nd International Conference on Genome Informatics (GIW2011), Haeundae Grand Hotel, Busan, Korea, Dec. 5-7, 2011.
     
  • 47. S. Kim, Y. Lee, K. W. Lee, "Homology Modeling of mouse TRESK and Prediction of Potassium Channel Blocker Binding Site through Molecular Docking Simulations" in the 22nd International Conference on Genome Informatics (GIW2011), Haeundae Grand Hotel, Busan, Korea, Dec. 5-7, 2011.
     
  • 46. S. Kim, Y. Lee, Y. Sohn, K. W. Lee, "Matrix Metalloproteinase-3 Inhibitor Design using 3D QSAR Pharmacophore Modeling" in the 22nd International Conference on Genome Informatics (GIW2011), Haeundae Grand Hotel, Busan, Korea, Dec. 5-7, 2011.
     
  • 45. Y. Sohn, Y. Lee, S. Kim, K. W. Lee, "Dynamic Pharmacophore Modeling of Peroxisome Proliferator-Activated Receptor gamma to Discover Novel Agonists" in the 22nd International Conference on Genome Informatics (GIW2011), Haeundae Grand Hotel, Busan, Korea, Dec. 5-7, 2011.
     
  • 44. V. Arulalapperumal, S. akkiah, S. Thangapandian, Y. Lee, G. Cao, K. W. Lee, "Chemical System Biology Approach: Functional site analysis to finding drug off-target effect of Aldose reductase inhibitors for Diabetic disease" in the 22nd International Conference on Genome Informatics (GIW2011), Haeundae Grand Hotel, Busan, Korea, Dec. 5-7, 2011.
     
  • 43. S. Kim, Y. Lee, M. Son, A. Baek, K. W. Lee, "Prediction of binding conformation between human acetylcholinesterase and cytochrome c using molecular modeling methods." in the 9th Asia Pacific Bioinformatics Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Songdo Convensia, Incheon, Korea, Jan. 11-14, 2011.
     
  • 42. A. Baek, Y. Sohn, S. Kim, Y. Lee, K. W. Lee, "Comparative studies of binding modes between fragaria vesca alcohol acetyltransferases (VAAT) and fragaria x ananassa alcohol acetyltransferases (SAAT) with same alcohol substrates by molecular modeling study." in the 9th Asia Pacific Bioinformatics Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Songdo Convensia, Incheon, Korea, Jan. 11-14, 2011.
     
  • 41. C. Park, S. Thangapandian, S. John, M. Son, Y. Lee, K. W. Lee, "Molecular dynamics simulation study of renin with inhibitors and its application in receptor-based pharmacophore modeling." in the 9th Asia Pacific Bioinformatics Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Songdo Convensia, Incheon, Korea, Jan. 11-14, 2011.
     
  • 40. M. Son, C. Park, S. Kim, Y. Lee, K. W. Lee, "Ligand and structure based pharmacophore models in the identification of potent substrates for NAD(P)H:Quinon oxidoreductase1 (NQO1)." in the 9th Asia Pacific Bioinformatics Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Songdo Convensia, Incheon, Korea, Jan. 11-14, 2011.
     
  • 39. Y. Lee, S. Kim, K. W. Lee, "Molecular modeling study of LPS recognition in TLR4-MD-2 complex." in the 9th Asia Pacific Bioinformatics Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Songdo Convensia, Incheon, Korea, Jan. 11-14, 2011.
     
  • 2010 

  • 38. A. Baek, S. Kim, M. Son, Y. Lee, K. W. Lee, "Homology homology modeling and molecular dynamics simulation study for arabidopsis thaliana small and basic intrinsic proteins (SIP)." in the 17th Annual Meeting of the Korean Biophysical Society, Yonsei-Samsung Library Building, University of Yonsei University, Korea, Jun. 25, 2010.
     
  • 37. S. Kim, Y. Lee, M. Son, A. Baek, K. W. Lee, "Binding mode analysis of human acetylcholinesterase with human cytochrome c using molecular docking methods." in the 17th Annual Meeting of the Korean Biophysical Society, Yonsei-Samsung Library Building, University of Yonsei University, Korea, Jun. 25, 2010.
     
  • 36. Y. Lee, S. Kim, K. W. Lee, "Macro-molecular docking study for human AChE WAT domain with human caveolin-1." in the 17th Annual Meeting of the Korean Biophysical Society, Yonsei-Samsung Library Building, University of Yonsei University, Korea, Jun. 25, 2010.
     
  • 35. S. Hwang, S. Thangapandian, Y. Lee, K. W. Lee, "Sonic hedgehog (SHH) inhibitor design by pharmacophore modeling and virtual screening." in the 105th spring meeting of the Korean Chemical Society, Songdo Convensia, Incheon, Korea, Apr. 29-30, 2010.
     
  • 34. Y. Lee, S. Kim, K. W. Lee, "Molecular docking study for glucokinase (GK) activators." in the 105th spring meeting of the Korean Chemical Society, Songdo Convensia, Incheon, Korea, Apr. 29-30, 2010.
     
  • 2009 

  • 33. C. Park, Y. Lee, K. W. Lee, "Homology modeling and molecular dynamics study for Arabidopsis thaliana CONSTANS B-box motifs." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 32. P. Lazar, S. Thangapandian, Y. Lee, K. W. Lee, "Computational approach to ensure the stability of the favorable ATP binding site in Hfq." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 31. M. Son, A. Baek, S. Kim, Y. Lee, K. W. Lee, "Three dimensional structure determination of sirt1 by homology modeling method." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 30. S. Kim, Y. Lee, M. Son, A. Baek, K. W. Lee, "Molecular docking study on molecular interaction between human acetylcholinesterase and cytochrome c." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 29. Y. Lee, S. Kim, W. Y. Bang, J. D. Bahk, K. W. Lee, "Developing a reliable 3D structure of Arabidopsis RelA/SpoT homolog 1." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 28. A. Baek, S. Kim, M. Son, Y. Lee, K. W. Lee, "Molecular modeling study on Arabidopsis thaliana small and basic intrinsic proteins (SIP)." in the Bioinfo 2009, The 10th International conference, Haeundae Grand Hotel, Busan, Korea, Nov. 4-6, 2009.
     
  • 27. Y. Sohn, Y. Lee, C. Park, S. Hwang, S. Kim, K. W. Lee, "Pharmacophore Identification of Human Peroxisome Proliferater-Activated Receptorγ." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 26. S. Hwang, Y. Lee, K. W. Lee, "Protein Engineering for New Epimerase through Flexible Molecular Docking Studies." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 25. A. Baek, S. Kim, Y. Lee, K. W. Lee, "3D Structure Determination of Arabidopsis thaliana Small and Basic Intrinsic Proteins (AtSIP) by Homology Modeling Method." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 24. C. Park, Y. Lee, K. W. Lee, "3D Structure Prediction of Full-length ANO1 using Multiple Fold-recognition Method." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 23. M. Son, S. Kim, Y. Lee, K. W. Lee, "Molecular Docking Study of Quinone Oxidoreductase (NQO) with Quinone Derivatives as New Inhibitor Candidates." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 22. S. Kim, Y. Lee, A. Baek, M. Son, K. W. Lee, "Interacting Site Prediction of Acetylcholinesterase with Cytochrome c by Molecular Docking and Molecular Dynamics Simulation Studies." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.
     
  • 21.Y. Lee, S. Kim, K. W. Lee, "Binding Mode Analysis of Human AChE with Human Caveolin-1 using Macro-molecular Docking Study." in The 103rd spring meeting of the Korean Chemical Society, COEX, Samsung City, Seoul, Korea, Apr. 16-17, 2009.

    2008
     
  • 20. A. Baek, S. Kim, Y. Lee, K. W. Lee, “Structural Comparison of Human Argonaute 2 Protein with the Other Three Human Argonaute Proteins.” in The 9th International Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University (CBNU), Cheongju City, Korea, Nov. 13-14, 2008.
     
  • 19. P. Lazar, Y. Lee, S. Kim, K. W. Lee, “Molecular Modeling Study for Apo and Holo form of a Novel Metalloenzyme-DOHH.” in The 9th International Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University (CBNU), Cheongju City, Korea, Nov. 13-14, 2008.
     
  • 18. M. Son, S. Kim, Y. Lee, K. W. Lee, “Molecular Docking Study of Quinone Oxidoreductase with Quinone Derivatives.” in The 9th International Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University (CBNU), Cheongju City, Korea, Nov. 13-14, 2008.
     
  • 17. S. Kim, Y. Lee, A. Baek, K. W. Lee, “Homology Modeling and Molecular Dynamics Simulation Study on TRESK-2 from Two Pore Domain Potassium Channel(K2P).” in The 9th International Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University (CBNU), Cheongju City, Korea, Nov. 13-14, 2008.
     
  • 16. Y. Lee, S. Kim, K. W. Lee, “Developing a Reliable 3D Structure of Arabidopsis CDSP32.” in The 9th International Conference of Korean Society for Bioinformatics and Systems Biology (KSBSB), Chungbuk National University (CBNU), Cheongju City, Korea, Nov. 13-14, 2008. [Outstanding Poster Award]
     
  • 15. S. Kim, Y. Lee, A. Baek, K. W. Lee, "Homology Modeling and Molecular Dynamics Simulation Study for TREK-2 Potassium Channel." in The 102nd National Meeting of Korean Chemical Society, International Convention Center(ICC), Jeju, Korea, Oct. 16-17, 2008.
     
  • 14. Y. Lee, S. Kim, K. W. Lee, "Structural Analysis of Arabidopsis NADPH-dependent Thioredoxin Reductase between Isotype A and C using Molecular Dynamics Simulations." in The 102nd National Meeting of Korean Chemical Society, International Convention Center(ICC), Jeju, Korea, Oct. 16-17, 2008.
     
  • 13. Y. Lee, W. Y. Bang, K. W. Lee, "Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 using Macro-molecular Docking Study." in The 101st Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 17-28, 2008.
     
  • 12. Y. Lee, S. Liu, K. W. Lee, "Molecular Modeling Study for Interaction Between urokinase-type Plasminogen Activator and Inhibitor." in The 101st Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 17-28, 2008.
     
  • 11. C. Park, Y. Lee, S. Kim, A. Baek, K. W. Lee, "Molecular Dynamics Simulation Study on Four Different PAZ Domains." in The 101st Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 17-28, 2008.
     
  • 10. A. Baek, J. Park, S. Kim, Y. Lee, C. Park, K. W. Lee, "Three Dimensional Structure Determination of Human Argonaute2 Protein by Homology Modeling Method." in The 101st Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 17-28, 2008.
     
  • 9.S. Kim, Y. Lee, C. Park, A. Baek, K. W. Lee, "Analysis of Four Domains Motion of A. aeolicus Argonaute Protein with siRNA using Molecular Dynamics Simulations." in The 101st Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 17-28, 2008.

    2007
     
  • 8. E. Lee, Y. Lee, J. D. Bahk, K. W. Lee, “Molecular Docking Study and Homology Modeling for the Indol oxygenase.” in The 8th International Conference of Korean Society for Bioinformatics(KSBI), KRIBB, Daejeon City, Korea, Nov. 15-16, 2007.
     
  • 7. Y. Lee, J. D. Bahk, K. W. Lee, “Structural Analysis of Bacillus subtilis Obg with Nucleotides using Molecular Dynamics Simulations.” in The 8th International Conference of Korean Society for Bioinformatics(KSBI), KRIBB, Daejeon City, Korea, Nov. 15-16, 2007.
     
  • 6. S. Kim, Y. Lee, J. D. Bahk, K. W. Lee, “Molecular Modeling Study on P. furiosus Argonaute and A.aeolicus Argonaute Proteins.” in The 8th International Conference of Korean Society for Bioinformatics(KSBI), KRIBB, Daejeon City, Korea, Nov. 15-16, 2007.
     
  • 5. Y. Lee, K. W. Lee, “Structural and Functional Insight for Ring Opening of Rare Sugar Molecules by D-Psicose 3-Epimerase.”, in The 99th Annual Meeting of Korean Chemical Society, COEX, Seoul, Korea, Apr. 19-20, 2007.
     
  • 4. Y. Lee, N. Krishnamoorthy, K. W. Lee, “Linking of Two Key Domains in AtTDX using Computer Modelling Methods.”, in The 99th Annual Meeting of Korean Chemical Society, COEX, Seoul, Korea, Apr. 19-20, 2007.
     
  • 3. J. Park, Y. Lee, K. W. Lee, “Molecular Modeling Study on Peroxisome Proliferator-Activated Receptor-γ and its Ligands.”, in The 99th Annual Meeting of Korean Chemical Society, COEX, Seoul, Korea, Apr. 19-20, 2007. [Poster Award]

    2006
     
  • 2. Y. Lee, N. Krishnan, K. W. Lee, “Molecular Dynamics Simulation Study on Adenosine Kinase.” , in The 7th International Conference of Korean Society for Bioinformatics(KSBI), POSTECH, Pohang City, Gyeongsang Buk-Do, Korea, Sept. 14-16, 2006.
     
  • 1. Y. Lee, N. Bharatham, K. Bharatham, E. Lee, K. W. Lee, "Docking Studies of Pharmacophore Model Based Adenosine Kinase Inhibitors.", in The 97th Annual Meeting of Korean Chemical Society, KINTEX, Goyang City, Kyeonggi-Do, Korea, Apr. 20-21, 2006.

 

RESEARCH INTERESTS

My current main projects

1) Investigation of conformational changes in EcTrxR to understand the electron transfer reaction mechanism and to further design new antibiotics using receptor based drug design.

 


2) Developing a rational approach for experimental data-driven docking through combining conventional docking (ZDOCK and HADDOCK) with COM pulling and distance restraint MD simulations to improve the protein-protein docking result.
 


3) Enhancing the enzyme catalytic activity using QM/MM MD simulation of the ligand in transition state.

 

SCIENCE 2010, 329(16), 309-313

The other projects

- ADO binding site and ATP binding site for adenosine kinase.

   
   

- Trx

- OBG

- DPE

- Pioneer

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