Publications



85. Adeel Malik, Juyong Lee, Jooyoung Lee, Community-Based Network Study of Protein-Carbohydrate Interactions inPlant Lectins Using Glycan Array Data, PLOS ONE, 9 (2014)
84. Keehyoung Joo, Juyong Lee, Sangjin Sim, Sun Young Lee, Kiho Lee, Seungryong Heo, In-Ho Lee, Sung Jong Lee and Jooyoung Lee, Protein structure modeling for CASP10 by multiple layers of global optimization, Proteins: Structure, Function, and Bioinformatics, 82, 188–195 (2013)
83. In-Ho Lee, Seung-Yeon Kim and Jooyoung Lee, Transition Pathway and Its Free-Energy Profile: A Protocol for Protein Folding Simulations,International Journal of Molecular Sciences, 14, 16058-16075 (2013)
82. Young Kwan Kim, Mi-Jeong Kwak, Bonsu Ku, Hye-Young Suh, Keehyoung Joo, Jooyoung Lee, Jae U. Jung and Byung-Ha Oh, Structural basis of intersubunit recognition in elongin BC–cullin 5–SOCS box ubiquitin–protein ligase complexes, Acta Crystallography, D69, 1587-1597 (2013)
81. Asim Okur, Benjamin T. Miller, Keehyoung Joo, Jooyoung Lee and Bernard R. Brooks, Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9,1115-1124 (2013)
80. Juyong Lee, Jooyoung Lee, Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction, PLOS ONE, 8 (2013)
79. Xinmiao Fu, Xiaodong Shi, Linxiang Yin, Jiafeng Liu, Keehyoung Joo, Jooyoung Lee and Zengyi Chang, Small Heat Shock Protein IbpB Acts as a Robust Chaperone in Living Cells by Hierarchically Activating Its Multi-type Substrate-binding Residues, JOURNAL OF BIOLOGICAL CHEMISTRY, 288, 11897-11906 (2013)
78. Juyong Lee, Steven P. Gross and Jooyoung Lee, Improved network community structure improves function prediction, SCIENTIFIC REPROTS, 3, 2197 (2013)
77. Juyong Lee, Steven P. Gross and Jooyoung Lee, Modularity optimization by conformational space annealing, PHYSICAL REVIEW E, 85, 056702 (2012)
76. In-Ho Lee, Seung-Yeon Kim and Jooyoung Lee, Folding Models of Mini-Protein FSD-1, JOURNAL OF PHYSICAL CHEMISTRY B, 116, 6916-6922 (2012)
75. Keehyoung Joo, Sung Jong Lee and Jooyoung Lee, Sann: Solvent accessibility prediction of proteins by nearest neighbor method, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80, 1791-1797 (2012)
74. Keehyoung Joo, Jinwoo Lee, Jooyoung Lee, Methods for Accurate Homology Modeling by Global Optimization, Chapter in "Methods for Homology Model Optimization" Humana Press, USA
73. Woong-Hee Shin, Lim Heo, Juyong Lee, Junsu Ko, Chaok Seok, Jooyoung Lee, LigDockCSA: Protein-Ligand Docking Using Conformational Space Annealing, JOURNAL OF COMPUTATIONAL CHEMISTRY, 32, 3226-3232 (2011)
72. Hahnbeom Park, Junsu Ko, Keehyoung Joo, Julian Lee, Chaok Seok, Jooyoung Lee, Refinement of protein termini in template-based modeling using conformational space annealing, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,  79,  2725-2734 (2011)
71. Juyong Lee, Jinhyuk Lee, Takeshi N Sasaki, Masaki Sasai, Chaok Seok, Jooyoung Lee, De novo protein structure prediction by dynamic fragment assembly and conformational space annealing, PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,  79,  2403-2417 (2011)
70. Haarin Chun, Keehyoung Joo, Jooyoung Lee, Hang-Cheol Shin, Design and efficient production of bovine enterokinase light chain with higher specificity in E. coli, BIOTECHNOLOGY LETTERS, 33, 1227-1232 (2011)
69. Joo-Hyun Seo, Dohyun Kyung, Keehyoung Joo, Jooyoung Lee, Byung-Gee Kim, Necessary and Sufficient Conditions for the Asymmetric Synthesis of Chiral Amines Using v-Aminotransferases, Biotechnol Bioeng. Volume 108, Issue 2, pages 253-263(2011)
68. In-Ho Lee, Seung-Yeon Kim, and Jooyoung Lee, Dynamic Folding Pathway Models of the Villin Headpiece Subdomain (HP-36) Structure J.Comput.Chem. 31, 57 (2009)
67.   Mina Oh, Keehyoung Joo, Jooyoung Lee, Protein-binding site prediction based on three-dimensional protein modeling, Proteins: Structure, Function, and Bioinformatics volume 77, Issue S9, Pages 152-156 (2009)
66.   Elmar Krieger, Keehyoung Joo, Jinwoo Lee, Jooyoung Lee , Srivatsan Raman, James Thompson, Mike Tyka, David Baker, and Kevin Karplus, Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8, Proteins: Structure, Function, and Bioinformatics volume 77, Issue S9, Pages 114-122 (2009)
65.   Keehyoung Joo, Jinwoo Lee, Joo-Hyun Seo, Kyoungrim Lee, Byung-Gee Kim, Jooyoung Lee, All-atom chain-building by optimizing MODELLER energy function using conformational space annealing, Proteins: Structure, Function, and Bioinformatics Volume 75, Issue 4, Pages: 1010-1023 (2009)
64.   Joo-Hyun Seo, Gang-Seong Lee, Juhan Kim, Byung-Kwan Cho, Keehyoung Joo, Jooyoung Lee , Byung-Gee Kim, Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening, Enzyme and Microbial Technology 45 218-225 (2009)
63.   Jae-Sung Woo, Jae-Hong Lim, Ho-Chul Shin, Min-Kang Suh, Bonsu Ku, Kwang-Hoon Lee, Keehyoung Joo, Howard Robinson, Jooyoung Lee , Sam-Yong Park, Nam-Chul Ha and Byung-Ha Oh, Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions, Cell, Volume 136, Issue 1, 85-96 (2009)
62.   Jinwoo Lee, Keehyung Joo, Seung-Yeon Kim and Jooyong Lee, Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing, JOURNAL OF COMPUTATIONAL CHEMISTRY Vol 29, 14, 2479-2484 (2008)
61.   Keehyoung Joo, Jinwoo Lee, Ilsoo Kim, Sung Jong Lee and Jooyoung Lee , Multiple Sequence Alignment by Conformational Space Annealing, BIOPHYSICAL JOURNAL Vol 95, 10, 4813-4819 (2008)
60.   Seung-Yeon Kim, Sung Jong Lee, and Jooyoung Lee , Ground-state energy and energy landscape of the Sherrington-Kirkpatrick spin glass, Phys.Rev.B, Vol. 76, 184412-1 - 184412-7 (2007).
59.   Michael Tress, Jianlin Cheng, Pierre Baldi, Keehyoung Joo, Jinwoo Lee, Joo-Hyun Seo, Jooyoung Lee , David Baker, Dylan Chivian, David Kim, and Iakes Ezkurdia, Assessment of predictions submitted for the CASP7 domain prediction category, Proteins, Vol. 69, 137-151 Suppl. 8 (2007).
58.   Keehyoung Joo, Jinwoo Lee, Sunjoong Lee, Joo-Hyun Seo, Sung Jong Lee, and Jooyoung Lee, High Accuracy Template Based Modeling by Global Optimization, Proteins, Vol. 69, 83-89 Suppl. 8 (2007).
57.   In-Ho Lee, Sukky Jun, Hanchul Kim, Seung-Yeon Kim, and Jooyoung Lee, Exploring dynamic pathways by action-derived molecular dynamics, INTERNATIONAL JOURNAL OF NANOTECHNOLOGY Vol. 3, 334-352 (2006).
56.   Hyeon S. Son, Seung-Yeon Kim, Jooyoung Lee, and Kyu-Kwang Han, Application of the multiensemble sampling to the equilibrium folding of proteins, Bioinformatics, Vol. 22, 1832-1837, (2006).
55.   Julian Lee, Seung-Yeon Kim and Jooyoung Lee Protein structure prediction based on fragment assembly and the beta-strand pairing energy function JOURNAL OF THE KOREAN PHYSICAL SOCIETY Volume: 46 Issue: 3 Pages: 707-712 Published: MAR (2005)
54.   Seung-Yeon Kim, Sang Bub Lee, and Jooyoung Lee, Structure optimization by conformational space annealing in an off-lattice protein model, Physical Review E Vol. 72, 011916, (2005).
53.   In-Ho Lee, Seung-Yeon Kim, and Jooyoung Lee, Dynamic folding pathway models of a-helix and b-hairpin structures, Chemical Physics Letters Vol. 412, 307-312, (2005)
52.   In-Ho Lee, Seung-Yeon Kim, and Jooyoung Lee, Dynamics of conformational isomerization of alanine dipeptide and valine dipeptide, Journal of the Korean Physical Society, Vol. 46, 601-605 (2005).
51.   Julian Lee, Seung-Yeon Kim, and Jooyoung Lee, Protein structure prediction based on fragment assembly and parameter optimization, BIOPHYSICAL CHEMISTRY Vol. 115, 209-214, (2005).
50.   MeeKyoung Song, Seung-Yeon Kim, and Jooyoung Lee, Understanding the structural characteristics of compstatin by conformational space annealing, BIOPHYSICAL CHEMISTRY Vol. 115, 201-207, (2005).
49.   Seung-Yeon Kim, Julian Lee, and Jooyoung Lee, Folding simulations of small proteins, BIOPHYSICAL CHEMISTRY Vol. 115, 195-200, (2005).
48.   Jaehyun Sim, Seung-Yeon Kim, and Jooyoung Lee , PPRODO: Prediction of Protein Domain Boundaries Using Neural Networks Proteins, Proteins: Structure, Function, and Genetics, Vol. 59, 627-632 (2005).
47.   Kyoungrim Lee, Jaehyun Sim, and Jooyoung Lee , Study of Protein-Protein Interaction Using Conformational Space Annealing, Proteins: Structure, Function, and Genetics, Vol. 60, 257-262 (2005)
46.   Kyoungrim Lee, Cezary Czaplewski, Kim Seung-Yeon, and Jooyoung Lee, An efficient molecular docking using conformational space annealing, J. Comput. Chem., Vol. 26, 78-87 (2005).
45.   Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon, Identification of the protein native structure by using a sequence-dependent feature in contact maps, Journal of the Korean Physical Society, Vol. 46, 625-630 (2005).
44.   Jaewoon Jung, Jooyoung Lee, and Hie-Tae Moon, Topological determinants of protein unfolding rates, Proteins: Structure, Function, and Genetics, Vol. 58, 389-395 (2005).
43.   Keehyung Joo, Ilsoo Kim, Seung-Yeon Kim, Julian Lee, Sung Jong Lee, and Jooyoung Lee, Prediction of the secondary structures of proteins by using PREDICT, a nearest neighbor method on pattern space, Journal of the Korean Physical Society, Vol. 45, 1441-1449 (2004).
42.   Julian Lee, Seung-Yeon Kim, Keehyung Joo, Ilsoo Kim, and Jooyoung Lee, Prediction of Protein Tertiary Structure Using PROFESY, a Novel Method Based on Fragment Assembly and Conformational Space Annealing, Proteins, Vol. 56, 704-714 (2004).
41.   Jaehyun Sim, Seung-Yeon Kim, A.Yoo, and Jooyoung Lee, Predicting the three dimensional structures of proteins: combined alignment approach, Journal of the Korean Physical Society, Vol. 44, 611-616 (2004).
40.   In-Ho Lee, and Jooyoung Lee, Accurate transition pathway calculation for rare events, Journal of the Korean Physical Society, Vol. 44, 605-610 (2004).
39.   Keehyung Joo, Julian Lee, Seung-Yeon Kim, Ilsoo Kim, Sung Jong Lee, and Jooyoung Lee, Profile-based nearest neighbor method for pattern recognition, Journal of the Korean Physical Society, Vol. 44, 599-604 (2004).
38.   Julian Lee, Seung-Yeon Kim, and Jooyoung Lee, Optimization of potential energy parameters for folding of several proteins, Journal of the Korean Physical Society, Vol. 44, 594-598 (2004).
37.   Seung-Yeon Kim, Sung Jong Lee, and Jooyoung Lee, The energy landscape of a BLN protein with beta hairpin shape, Journal of the Korean Physical Society, Vol. 44, 589-593 (2004).
36.   Julian Lee, Seung-Yeon Kim, and Jooyoung Lee, Design of a Protein Potential Energy Land scape by Parameter Optimization, J.Phys.Chem.B, Vol. 108, 4525-4534 (2004).
35.   Seung-Yeon Kim, Julian Lee, and Jooyoung Lee, Folding of small proteins using a single continuous potential, J.Chem.Phys., Vol. 120, 8271-8276 (2004).
34.   In-Ho Lee, H.Kim, and Jooyoung Lee, Dynamic pathway model for the formation of C60, J.Chem.Phys., Vol. 120, 4672-4676 (2004).
33.   Seung-Yeon Kim, Sung Jong Lee, and Jooyoung Lee, Conformational space annealing and an off-lattice frustrated model protein, J.Chem.Phys., Vol. 119, 10274-10279 (2003).
32.   Julian Lee, In-Ho Lee, and Jooyoung Lee, Unbiased global optimization of Lennard Jones clusters for N <= 201 by conformational space annealing method, Phys.Rev.Lett., Vol. 91, 080201 (2003).
31.   In-Ho Lee, Jooyoung Lee, and Sangsan Lee, Kinetic energy control in the action derived molecular dynamics simulations, Phys.Rev.B, Vol. 68, 064303 (2003).
30.   Myoung Kwan Ko, Sung Jong Lee, Jooyoung Lee, and Bongsoo Kim, Vortex patterns and infinite degeneracy in the uniformly frustrated XY models and lattice coulomb gas, Phys.Rev.E, Vol. 67, 046120 (2003).
29.   Sung Jong Lee, Bongsoo Kim, and Jooyoung Lee, Infinite ground state degeneracy and glassy dynamics in the frustrated XY model and lattice coulomb gas with f =1/6, Physica A, Vol. 315, 314-320 (2002).
28.   Harold A.Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R.Ripoll, William J.Wedemeyer, and Yelena A.Arnautova, Evolution of physics based methodology for exploring the conformational energy landscape of proteins, J.Comput.Chem., Vol. 23, 28-34 (2002).
27.   Julian Lee, Kibeom Park, and Jooyoung Lee, Full optimization of linear parameters of a united residue protein potential, J.Phys.Chem.B, Vol. 106, 11647-11657(2002).
26.   Jaroslaw Pillardy, Cezary Czaplewski, Adam Liwo, Jooyoung Lee, Daniel R.Ripoll, Rajmund Kamierkiewicz, Stanislaw Oldziej, William J.Wedemeyer, Kenneth D.Gibson, Yelena A.Arnautova, Jeffrey Saunders, Yuan-Jie Ye, and Harold A.Scheraga, Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proc.Natl.Acad.Sci., U.S.A., Vol. 98, 2329-2333 (2001).
25.   Jaroslaw Pillardy, Cezary Czaplewski, Adam Liwo, William J.Wedemeyer, Jooyoung Lee, Daniel R.Ripoll, P.Arlukowicz, S.Oldziej, Y.A.Arnautova, and Harold A.Scheraga, Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha, beta and alpha/beta structural classes, J.Phys.Chem.B, Vol. 105, 7299-7311 (2001).
24.   Jooyoung Lee, Daniel R.Ripoll, Cezary Czaplewski, Jaroslaw Pillardy, William J.Wedemeyer, and Harold A.Scheraga, Optimization of parameters in macromolecular potential energy functions by conformational space annealing, J.Phys.Chem.B, Vol. 105, 7291-7298 (2001).
23.   Jooyoung Lee, Adam Liwo, Daniel R.Ripoll, Jaroslaw Pillardy, Jeffrey A.Saunders, Kenneth D.Gibson, and Harold A.Scheraga, Hierarchical energy based approach to protein structure prediction; blind test evaluation with CASP3 targets, Int.J.Quant.Chem., Vol. 77, 90-117 (2000).
22.   Jooyoung Lee, Jaroslaw Pillardy, Cezary Czaplewski, Yelena Arnautova, Daniel R.Ripoll, Adam Liwo, Kenneth D.Gibson, Ryszard J.Wawak, and Harold A.Scheraga, Efficient parallel algorithms in global optimization of potential energy function, Compt.Phys.Comm., Vol. 128, 399-411 (2000).
21.   Harold A.Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan JieYe, Adam Liwo, and Daniel R.Ripoll, Surmounting the Multiple Minima Problem in Protein Folding, J.Global Opt., Vol. 15, 235-260 (1999).
20.   Jooyoung Lee, Adam Liwo, Daniel R.Ripoll, Jaroslaw Pillardy, and Harold A.Scheraga, Calculation of Protein Conformation by Global Optimization of a potential energy function, Proteins: Struc.,Func., and Gen., Suppl. Vol. 3, 204-208 (1999).
19.   Jooyoung Lee and Harold A.Scheraga, Conformational space annealing by parallel computations: extensive conformational search of Met-enkephalin and of the 20 residue membrane bound portion of melittin, Int.J.Quant.Chem., Vol. 75, 255-265 (1999).
18.   Adam Liwo, Jooyoung Lee, Daniel R.Ripoll, Jaroslaw Pillardy, and Harold A.Scheraga, Protein structure prediction by global optimization of a potential energy function, Proc.Natl.Acad.Sci., U.S.A., Vol. 96, 5482-5485 (1999).
17.   Jooyoung Lee, Adam Liwo, and Harold A.Scheraga, Energy based de novo protein folding by conformational space annealing and an off-lattice united residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K, Proc.Natl.Acad.Sci., U.S.A., Vol. 96, 2025-2030 (1999).
16.   Jooyoung Lee, Harold A.Scheraga, and S.Rackovsky, Conformational analysis of the 20 residue membrane bound portion of melittin by conformational space annealing, Biopolymers, Vol. 46, 103-115 (1998).
15.   Jooyoung Lee, Harold A.Scheraga, and S.Rackovsky, New Optimization Method for Conformational Energy Calculations on Polypeptides: Conformational Space Annealing, J.Comput.Chem., Vol. 18, 1222-1232 (1997).
14.   Jooyoung Lee, Harold A.Scheraga, and S.Rackovsky, Computational Study of Packing a Collagen-like molecule: Quasi-hexagonal vs. "Smith" Collagen Microfibril Model, Biopolymers, Vol. 40, 595-607 (1996).
13.   Jooyoung Lee, M.A.Novotny, and P.A.Rikvold, Method to study relaxation of metastable phase: Macroscopic mean-field dynamics, Phys.Rev.E, Vol. 50, 356-372 (1995).
12.   H.Meirovitch, E.Meirovitch, and Jooyoung Lee, New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. 1. The Relative Contribution of Low Energy Microstates to the Partition Function, J.Phys.Chem., Vol. 99, 4847-4854 (1995).
11.   Jooyoung Lee and M.Y.Choi, Optimization by Multicanonical Annealing and the Traveling Salesman Problem, Phys.Rev.E, Vol. 50, Rapid Communications, R651-R654 (1994).
10.   Jooyoung Lee, New Monte Carlo Algorithm : Entropic Sampling, Phys.Rev.Lett., Vol. 71, 211-214 (1993) ; Erratum Vol. 71, 2353 (1993).
09.   Jooyoung Lee and Katherine J.Strandburg, First Order Melting Transition of the Hard Disk System, Phys.Rev.B, Vol. 46, Rapid Communications, 11190-11193 (1992).
08.   Jooyoung Lee, E.Granato, and J.M.Kosterlitz, Non-universal behavior and first-order transitions in a coupled XY Ising model, Phys.Rev.B, Vol. 44, 4819-4831 (1991).
07.   Jooyoung Lee, J.M.Kosterlitz, and E.Granato, Monte Carlo Study of frustrated XY models on a triangular and square lattice, Phys.Rev.B, Vol. 43, Rapid Communications, 11531-11534 (1991).
06.   E.Granato, J.M.Kosterlitz, Jooyoung Lee, and M.P.Nightingale, Phase transitions in coupled XY Ising systems, Phys.Rev.Lett., Vol. 66, 1090-1093 (1991).
05.   Jooyoung Lee and J.M.Kosterlitz, Finite Size Scaling and Monte Carlo Simulations of First Order Phase Transitions, Phys.Rev.B, Vol. 43, 3265-3277 (1991).
04.   Jooyoung Lee and J.M.Kosterlitz, Three dimensional q-state Potts model : Monte Carlo study near q=3, Phys.Rev.B, Vol. 43, Rapid Communications, 1268-1271 (1991).
03.   Jooyoung Lee and J.M.Kosterlitz, New Numerical Method to Study Phase Transitions, Phys.Rev.Lett., Vol. 65, 137-140 (1990).
02.   Jooyoung Lee, Doochul Kim and Peter M.Levy, Phase Diagram for the Cubic Model of HoP in a Magnetic Field, Journal of the Korean Physical Society, Vol. 18, 7-11 (1985).
01.   Jong Hoon Oh, Jooyoung Lee, and Doochul Kim, Phase Transition of the FCC Ising Ferromagnet with Competing Interaction, Journal of the Korean Physical Society, Vol. 17, 122-125 (1984).