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Jooyoung Lee, Ph.D. - Publications

Affiliations: 
University of Florida, Gainesville, Gainesville, FL, United States 
Area:
advanced electronic materials
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Year Citation  Score
2019 Choi K, Chun J, Han K, Park S, Soh H, Kim J, Lee J, Lee HJ, Im JP, Kim JS. Risk of Anxiety and Depression in Patients with Inflammatory Bowel Disease: A Nationwide, Population-Based Study. Journal of Clinical Medicine. 8. PMID 31083476 DOI: 10.3390/jcm8050654  0.48
2019 Lee J, Jo DH, Kim JH, Cho CS, Han JE, Kim Y, Park H, Yoo SH, Yu YS, Moon HE, Park HR, Kim DG, Kim JH, Paek SH. Development of a patient-derived xenograft model of glioblastoma via intravitreal injection in mice. Experimental & Molecular Medicine. 51: 43. PMID 30992429 DOI: 10.1038/s12276-019-0241-3  0.32
2019 Manavalan B, Kuwajima K, Lee J. PFDB: A standardized protein folding database with temperature correction. Scientific Reports. 9: 1588. PMID 30733462 DOI: 10.1038/s41598-018-36992-y  0.36
2019 Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, Lee J, Im W. CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates. Glycobiology. PMID 30689864 DOI: 10.1093/glycob/cwz003  0.44
2018 Soh H, Chun J, Han K, Park S, Choi G, Kim JH, Lee J, Im JP, Kim JS. Increased Risk of Herpes Zoster in Young and Metabolically Healthy Patients with Inflammatory Bowel Disease: A Nationwide Population-based Study. Gut and Liver. PMID 30602222 DOI: 10.5009/gnl18304  0.48
2018 Park S, Chun J, Han KD, Soh H, Choi K, Kim JH, Lee J, Lee C, Im JP, Kim JS. Increased end-stage renal disease risk in patients with inflammatory bowel disease: A nationwide population-based study. World Journal of Gastroenterology. 24: 4798-4808. PMID 30479466 DOI: 10.3748/wjg.v24.i42.4798  0.48
2018 Bhak G, Lee S, Kim TH, Lee JH, Yang JE, Joo K, Lee J, Char K, Paik SR. Morphological Evaluation of Meta-stable Oligomers of α-Synuclein with Small-Angle Neutron Scattering. Scientific Reports. 8: 14295. PMID 30250173 DOI: 10.1038/s41598-018-32655-0  0.44
2018 Joo K, Heo S, Joung I, Hong SH, Lee SJ, Lee J. Data-Assisted Protein Structure Modeling by Global Optimization in CASP12. Proteins. PMID 29341255 DOI: 10.1002/prot.25457  0.44
2017 Hong SH, Joung I, Flores-Canales JC, Manavalan B, Cheng Q, Heo S, Kim JY, Lee SY, Nam M, Joo K, Lee IH, Lee SJ, Lee J. Protein Structure Modeling and Refinement by Global Optimization in CASP12. Proteins. PMID 29159837 DOI: 10.1002/prot.25426  0.64
2017 Park J, Kim MS, Joo K, Lee J, Shin DH. An artificially constructed dimer through deformation of a short zinc-binding loop. Biochimica Et Biophysica Acta. PMID 29122686 DOI: 10.1016/j.bbapap.2017.11.002  0.48
2017 Karczyńska AS, Czaplewski C, Krupa P, Mozolewska MA, Joo K, Lee J, Liwo A. Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. Journal of Computational Chemistry. PMID 28940211 DOI: 10.1002/jcc.25070  0.44
2017 Kwak MJ, Kim JD, Kim H, Kim C, Bowman JW, Kim S, Joo K, Lee J, Jin KS, Kim YG, Lee NK, Jung JU, Oh BH. Architecture of the type IV coupling protein complex of Legionella pneumophila. Nature Microbiology. 2: 17114. PMID 28714967 DOI: 10.1038/nmicrobiol.2017.114  0.48
2017 Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nature Communications. 8: 15443. PMID 28548089 DOI: 10.1038/ncomms15443  0.64
2017 Manavalan B, Lee J. SVMQA: Support-vector-machine-based protein single-model quality assessment. Bioinformatics (Oxford, England). PMID 28419290 DOI: 10.1093/bioinformatics/btx222  0.36
2017 Heo S, Lee J, Joo K, Shin HC, Lee J. Protein Loop Structure Prediction using Conformational Space Annealing. Journal of Chemical Information and Modeling. PMID 28398048 DOI: 10.1021/acs.jcim.6b00742  0.44
2016 Mozolewska MA, Krupa P, Zaborowski B, Liwo A, Lee J, Joo K, Czaplewski C. Use of Restraints from Consensus Fragments of Multiple Server Models to Enhance Protein-Structure Prediction Capability of the UNRES Force Field. Journal of Chemical Information and Modeling. PMID 27749055 DOI: 10.1021/acs.jcim.6b00189  0.44
2016 Park J, Kim MS, Joo K, Jhon GJ, Berry EA, Lee J, Shin DH. Crystal Structure of Hypothetical Fructose-Specific EIIB from Escherichia coli. Molecules and Cells. PMID 27215198 DOI: 10.14348/molcells.2016.0055  0.48
2016 Lee J, Hwang SW, Kim J, Kang J, Kang GH, Park KJ, Im JP, Kim JS. Multiple Polypoid Angiodysplasia with Obscure Overt Bleeding. Clinical Endoscopy. 49: 91-96. PMID 26855931 DOI: 10.5946/ce.2016.49.1.91  0.32
2015 Joo K, Joung I, Cheng Q, Lee SJ, Lee J. Contact assisted protein structure modeling by global optimization in CASP11. Proteins. PMID 26677100 DOI: 10.1002/prot.24975  0.44
2015 Oh YJ, Lee IH, Kim S, Lee J, Chang KJ. Dipole-allowed direct band gap silicon superlattices. Scientific Reports. 5: 18086. PMID 26656482 DOI: 10.1038/srep18086  0.64
2015 Lee J, Joo K, Brooks BR, Lee J. The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential. Journal of Chemical Theory and Computation. 11: 3211-3224. PMID 26575758 DOI: 10.1021/acs.jctc.5b00268  0.44
2015 Joung I, Lee SY, Cheng Q, Kim JY, Joo K, Lee SJ, Lee J. Template Free Modeling by LEE and LEER in CASP11. Proteins. PMID 26474186 DOI: 10.1002/prot.24944  0.48
2015 Lee IH, Kim SY, Lee J. A Folding Pathway Model of Mini-Protein BBA5. Biomed Research International. 2015: 828095. PMID 26457304 DOI: 10.1155/2015/828095  0.92
2015 Joo K, Joung I, Lee J, Lee J, Lee W, Brooks B, Lee SJ, Lee J. Protein structure determination by conformational space annealing using NMR geometric restraints. Proteins. PMID 26454251 DOI: 10.1002/prot.24941  0.44
2015 Joo K, Joung I, Lee SY, Kim JY, Cheng Q, Manavalan B, Joung JY, Heo S, Lee J, Nam M, Lee IH, Lee SJ, Lee J. Template based protein structure modeling by global optimization in CASP11. Proteins. PMID 26329522 DOI: 10.1002/prot.24917  0.64
2015 Lee J, Lee SJ, Ahn KH, Lee SJ. Bimodal colloid gels of highly size-asymmetric particles. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 92: 012313. PMID 26274168  0.32
2015 Krupa P, Mozolewska MA, Joo K, Lee J, Czaplewski C, Liwo A. Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. Journal of Chemical Information and Modeling. 55: 1271-81. PMID 25965196 DOI: 10.1021/acs.jcim.5b00117  0.44
2015 Lee J, Lee K, Joung I, Joo K, Brooks BR, Lee J. Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. Bmc Bioinformatics. 16: 94. PMID 25886990 DOI: 10.1186/s12859-015-0526-z  0.44
2014 Cho UJ, Lee J, Kim HW, Lee JS, Joo YH, Kim SY, Kim CY, Shin YW. Age structure at diagnosis affects aggression in a psychiatric inpatient population: age structure affecting inpatient aggression. Psychiatry Research. 220: 1059-63. PMID 25453640 DOI: 10.1016/j.psychres.2014.09.022  0.92
2014 Manavalan B, Lee J, Lee J. Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. Plos One. 9: e106542. PMID 25222008 DOI: 10.1371/journal.pone.0106542  0.36
2014 Kaname T, Ki CS, Niikawa N, Baillie GS, Day JP, Yamamura K, Ohta T, Nishimura G, Mastuura N, Kim OH, Sohn YB, Kim HW, Cho SY, Ko AR, Lee JY, ... ... Lee J, et al. Heterozygous mutations in cyclic AMP phosphodiesterase-4D (PDE4D) and protein kinase A (PKA) provide new insights into the molecular pathology of acrodysostosis. Cellular Signalling. 26: 2446-59. PMID 25064455 DOI: 10.1016/j.cellsig.2014.07.025  0.44
2014 Lee J, Kwon YY, Choi EH, Park J, Yoon H, Kim H. Enhancement of light-extraction efficiency of organic light-emitting diodes using silica nanoparticles embedded in TiO₂ matrices. Optics Express. 22: A705-14. PMID 24922378  0.48
2014 Hong SW, Shin JS, Moon JH, Kim YS, Lee J, Choi EK, Ha SH, Lee DH, Chung HN, Kim JE, Kim KP, Hong YS, Lee JL, Lee WJ, Choi EK, ... Lee JS, et al. NVP-BEZ235, a dual PI3K/mTOR inhibitor, induces cell death through alternate routes in prostate cancer cells depending on the PTEN genotype. Apoptosis : An International Journal On Programmed Cell Death. 19: 895-904. PMID 24652480 DOI: 10.1007/s10495-014-0973-4  0.56
2014 Seo JH, Park J, Kim EM, Kim J, Joo K, Lee J, Kim BG. Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. Computational Biology and Chemistry. 48: 64-70. PMID 24378653 DOI: 10.1016/j.compbiolchem.2013.11.004  0.48
2014 Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, Lee IH, Lee SJ, Lee J. Protein structure modeling for CASP10 by multiple layers of global optimization. Proteins. 82: 188-95. PMID 23966235 DOI: 10.1002/prot.24397  0.64
2013 Park S, Lee J, Lee SY, Bae JW, Hwang KK, Kim DW, Cho MC, Kim SM. Acute Profound Thrombocytopenia after Using Abciximab for No-Reflow during Primary Percutaneous Coronary Intervention for ST-Segment Elevation Myocardial Infarction. Korean Circulation Journal. 43: 557-60. PMID 24044015 DOI: 10.4070/kcj.2013.43.8.557  0.48
2013 Lee IH, Kim SY, Lee J. Transition pathway and its free-energy profile: a protocol for protein folding simulations. International Journal of Molecular Sciences. 14: 16058-75. PMID 23917881 DOI: 10.3390/ijms140816058  0.92
2013 Kim YK, Kwak MJ, Ku B, Suh HY, Joo K, Lee J, Jung JU, Oh BH. Structural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes. Acta Crystallographica. Section D, Biological Crystallography. 69: 1587-97. PMID 23897481 DOI: 10.1107/S0907444913011220  0.44
2013 Kim S, Ghafoor K, Lee J, Feng M, Hong J, Lee DU, Park J. Bacterial inactivation in water, DNA strand breaking, and membrane damage induced by ultraviolet-assisted titanium dioxide photocatalysis. Water Research. 47: 4403-11. PMID 23764591 DOI: 10.1016/j.watres.2013.05.009  0.48
2013 Shin K, Yun Y, Yi S, Lee HG, Cho JC, Suh KD, Lee J, Park J. Biofilm-forming ability of Staphylococcus aureus strains isolated from human skin. Journal of Dermatological Science. 71: 130-7. PMID 23664186 DOI: 10.1016/j.jdermsci.2013.04.004  0.48
2013 Okur A, Miller BT, Joo K, Lee J, Brooks BR. Generating reservoir conformations for replica exchange through the use of the conformational space annealing method. Journal of Chemical Theory and Computation. 9: 1115-1124. PMID 23585739 DOI: 10.1021/ct300996m  0.44
2013 Fu X, Shi X, Yin L, Liu J, Joo K, Lee J, Chang Z. Small heat shock protein IbpB acts as a robust chaperone in living cells by hierarchically activating its multi-type substrate-binding residues. The Journal of Biological Chemistry. 288: 11897-906. PMID 23486475 DOI: 10.1074/jbc.M113.450437  0.44
2012 Joo K, Lee SJ, Lee J. Sann: solvent accessibility prediction of proteins by nearest neighbor method. Proteins. 80: 1791-7. PMID 22434533 DOI: 10.1002/prot.24074  0.44
2012 Lee IH, Kim SY, Lee J. Folding models of mini-protein FSD-1. The Journal of Physical Chemistry. B. 116: 6916-22. PMID 22417236 DOI: 10.1021/jp300074f  0.92
2012 Joo K, Lee J, Lee J. Methods for accurate homology modeling by global optimization. Methods in Molecular Biology (Clifton, N.J.). 857: 175-88. PMID 22323221 DOI: 10.1007/978-1-61779-588-6_7  0.44
2011 Park H, Ko J, Joo K, Lee J, Seok C, Lee J. Refinement of protein termini in template-based modeling using conformational space annealing. Proteins. 79: 2725-34. PMID 21755541 DOI: 10.1002/prot.23101  0.44
2011 Chun H, Joo K, Lee J, Shin HC. Design and efficient production of bovine enterokinase light chain with higher specificity in E. coli. Biotechnology Letters. 33: 1227-32. PMID 21331584 DOI: 10.1007/s10529-011-0562-3  0.44
2011 Seo JH, Kyung D, Joo K, Lee J, Kim BG. Necessary and sufficient conditions for the asymmetric synthesis of chiral amines using ω-aminotransferases. Biotechnology and Bioengineering. 108: 253-63. PMID 20824676 DOI: 10.1002/bit.22930  0.44
2010 Lee IH, Kim SY, Lee J. Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure. Journal of Computational Chemistry. 31: 57-65. PMID 19412905 DOI: 10.1002/jcc.21288  0.92
2009 Oh M, Joo K, Lee J. Protein-binding site prediction based on three-dimensional protein modeling. Proteins. 77: 152-6. PMID 19768678 DOI: 10.1002/prot.22572  0.44
2009 Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins. 77: 114-22. PMID 19768677 DOI: 10.1002/prot.22570  0.44
2009 Woo JS, Lim JH, Shin HC, Suh MK, Ku B, Lee KH, Joo K, Robinson H, Lee J, Park SY, Ha NC, Oh BH. Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions. Cell. 136: 85-96. PMID 19135891 DOI: 10.1016/j.cell.2008.10.050  0.44
2009 Joo K, Lee J, Seo JH, Lee K, Kim BG, Lee J. All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins. 75: 1010-23. PMID 19089941 DOI: 10.1002/prot.22312  0.44
2008 Joo K, Lee J, Kim I, Lee SJ, Lee J. Multiple sequence alignment by conformational space annealing. Biophysical Journal. 95: 4813-9. PMID 18689453 DOI: 10.1529/biophysj.108.129684  0.44
2008 Lee J, Joo K, Kim SY, Lee J. Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing. Journal of Computational Chemistry. 29: 2479-84. PMID 18470971 DOI: 10.1002/jcc.20995  0.92
2007 Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins. 69: 83-9. PMID 17894332 DOI: 10.1002/prot.21628  0.44
2007 Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/prot.21675  0.44
2006 Son HS, Kim SY, Lee J, Han KK. Application of the multiensemble sampling to the equilibrium folding of proteins. Bioinformatics (Oxford, England). 22: 1832-7. PMID 16766555 DOI: 10.1093/bioinformatics/btl282  0.92
2005 Kim SY, Lee SB, Lee J. Structure optimization by conformational space annealing in an off-lattice protein model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 011916. PMID 16090010 DOI: 10.1103/PhysRevE.72.011916  0.92
2005 Lee K, Sim J, Lee J. Study of protein-protein interaction using conformational space annealing. Proteins. 60: 257-62. PMID 15981254 DOI: 10.1002/prot.20567  0.48
2005 Sim J, Kim SY, Lee J. PPRODO: prediction of protein domain boundaries using neural networks. Proteins. 59: 627-32. PMID 15789433 DOI: 10.1002/prot.20442  0.92
2005 Lee J, Kim SY, Lee J. Protein structure prediction based on fragment assembly and parameter optimization. Biophysical Chemistry. 115: 209-14. PMID 15752606 DOI: 10.1016/j.bpc.2004.12.046  0.92
2005 Song MK, Kim SY, Lee J. Understanding the structural characteristics of compstatin by conformational space annealing. Biophysical Chemistry. 115: 201-7. PMID 15752605 DOI: 10.1016/j.bpc.2004.12.039  0.92
2005 Kim SY, Lee J, Lee J. Folding simulations of small proteins. Biophysical Chemistry. 115: 195-200. PMID 15752604 DOI: 10.1016/j.bpc.2004.12.040  0.92
2005 Lee K, Czaplewski C, Kim SY, Lee J. An efficient molecular docking using conformational space annealing. Journal of Computational Chemistry. 26: 78-87. PMID 15538770 DOI: 10.1002/jcc.20147  0.92
2004 Lee J, Kim SY, Joo K, Kim I, Lee J. Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing. Proteins. 56: 704-14. PMID 15281124 DOI: 10.1002/prot.20150  0.92
2004 Kim SY, Lee J, Lee J. Folding of small proteins using a single continuous potential. The Journal of Chemical Physics. 120: 8271-6. PMID 15267747 DOI: 10.1063/1.1689643  0.92
2004 Lee IH, Kim H, Lee J. Dynamic pathway model for the formation of C(60). The Journal of Chemical Physics. 120: 4672-6. PMID 15267326 DOI: 10.1063/1.1645776  0.64
2003 Lee J, Lee IH, Lee J. Unbiased global optimization of Lennard-Jones clusters for N < or =201 using the conformational space annealing method. Physical Review Letters. 91: 080201. PMID 14525223 DOI: 10.1103/PhysRevLett.91.080201  0.64
2003 Ko MK, Lee SJ, Lee J, Kim B. Vortex patterns and infinite degeneracy in the uniformly frustrated XY models and lattice Coulomb gas. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 67: 046120. PMID 12786449  0.32
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