S-Space

Browse

Author

Jump to a point in the index

Or type in a year

Sort by
In order
Results/Page
Authors/record

Showing results 1 to 56 of 56

Issue Date	Title / Author(s) / Citation	File
2008-02	Structural basis of functional conversion of a floral repressor to an activator: A molecular dynamics simulation study Kang, Suk Ki; Lee, Ju Yong; Lee, Myeong Sup; Seok, Cha Ok Bulletin of the Korean Chemical Society, Vol.29 No.2, pp.408-412	DOI
2008-02	A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect Lee, Ju Yong; Seok, Chaok PROTEINS : Structure, Function, and Bioinformatics, Vol.70 No.3, pp.1074-1083	DOI
2010-06	Cooperativity and Specificity of Cys2His2 Zinc Finger Protein-DNA Interactions: A Molecular Dynamics Simulation Study Lee, Ju Yong; Kim, Jin-Soo; Seok, Chaok The Journal of Physical Chemistry B, Vol.114 No.22, pp.7662-7671	DOI
2010-08	Transition between B-DNA and Z-DNA: Free Energy Landscape for the B-Z Junction Propagation Lee, Ju Yong; Kim, Yang Gyun; Kim, Kyeong Kyu; Seok, Chaok The Journal of Physical Chemistry B, Vol.114 No.30, pp.9872-9881	DOI
2011-08	De novo protein structure prediction by dynamic fragment assembly and conformational space annealing Lee, Ju Yong; Lee, Jin Hyuk; Sasaki, Takeshi N.; Sasai, Masaki; Seok, Chaok; Lee, Joo Young PROTEINS : Structure, Function, and Bioinformatics, Vol.79 No.8, pp.2403-2417	DOI
2011-11	LigDockCSA: Protein-Ligand Docking Using Conformational Space Annealing Shin, Woong-Hee; Heo, Lim; Lee, Ju Yong; Ko, Jun Su; Seok, Chaok; Lee, Joo Young Journal of Computational Chemistry, Vol.32 No.15, pp.3226-3232	DOI
2012-05	Modularity optimization by conformational space annealing Lee, Ju Yong; Gross, Steven P.; Lee, Joo Young Physical Review e, Vol.85 No.5, p. 056702	DOI
2012-11	Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA Lee, Youn Kyoung; Lee, Ju Yong; Choi, Jung Hyun; Seok, Chaok Bulletin of the Korean Chemical Society, Vol.33 No.11, pp.3719-3726	DOI
2013-04	What stabilizes close arginine pairing in proteins? Lee, Dong Seon; Lee, Ju Yong; Seok, Chaok Physical Chemistry Chemical Physics, Vol.15 No.16, pp.5844-5853	DOI
2013-04	Hidden Information Revealed by Optimal Community Structure from a Protein-Complex Bipartite Network Improves Protein Function Prediction Lee, Ju Yong; Lee, Joo Young PLoS ONE, Vol.8 No.4, p. e60372	DOI
2013-07	Improved network community structure improves function prediction Lee, Ju Yong; Gross, Steven P.; Lee, Joo Young Scientific Reports, Vol.3, p. 2197	DOI
2014-02	Protein structure modeling for CASP10 by multiple layers of global optimization Joo, Kee Hyoung; Lee, Ju Yong; Sim, Sang Jin; Lee, Sun Young; Lee, Ki Ho; Heo, Seung Ryong; Lee, In-Ho; Lee, Sung Jong; Lee, Joo Young PROTEINS : Structure, Function, and Bioinformatics, Vol.82, pp.188-195	DOI
2014-04	Community-Based Network Study of Protein-Carbohydrate Interactions in Plant Lectins Using Glycan Array Data Malik, Adeel; Lee, Ju Yong; Lee, Joo Young PLoS ONE, Vol.9 No.4, p. e95480	DOI
2014-07	Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange Lee, Ju Yong; Miller, Benjamin T.; Damjanovic, Ana; Brooks, Bernard R. Journal of Chemical Theory and Computation, Vol.10 No.7, pp.2738-2750	DOI
2014-09	Random Forest-Based Protein Model Quality Assessment (RFMQA) Using Structural Features and Potential Energy Terms Manavalan, Balachandran; Lee, Ju Yong; Lee, Jooyoung PLoS ONE, Vol.9 No.9, p. e106542	DOI
2015-03	Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest Lee, Ju Yong; Lee, Ki Ho; Joung, In Suk; Joo, Kee Hyoung; Brooks, Bernard R.; Lee, Joo Young BMC Bioinformatics, Vol.16, p. 94	DOI
2015-06	Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method Lee, Ju Yong; Miller, Benjamin T.; Damjanovic, Ana; Brooks, Bernard R. Journal of Chemical Theory and Computation, Vol.11 No.6, pp.2560-2574	DOI
2015-07	The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential Lee, Ju Yong; Joo, Kee Hyoung; Brooks, Bernard R.; Lee, Joo Young Journal of Chemical Theory and Computation, Vol.11 No.7, pp.3211-3224	DOI
2016-01	Computational scheme for pH-dependent binding free energy calculation with explicit solvent Lee, Ju Yong; Miller, Benjamin T.; Brooks, Bernard R. Protein Science, Vol.25 No.1, pp.231-243	DOI
2016-09	Template based protein structure modeling by global optimization in CASP11 Joo, Keehyoung; Joung, Insuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Ju Yong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung PROTEINS : Structure, Function, and Bioinformatics, Vol.84, pp.221-232	DOI
2016-11	Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge Koenig, Gerhard; Pickard, Frank C.; Huang, Jing; Simmonett, Andrew C.; Tofoleanu, Florentina; Lee, Ju Yong; Dral, Pavlo O.; Prasad, Samarjeet; Jones, Michael; Shao, Yihan; Thiel, Walter; Brooks, Bernard R. Journal of Computer-Aided Molecular Design, Vol.30 No.11, pp.989-1006	DOI
2016-11	Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections Pickard, Frank C.; Koenig, Gerhard; Tofoleanu, Florentina; Lee, Ju Yong; Simmonett, Andrew C.; Shao, Yihan; Ponder, Jay W.; Brooks, Bernard R. Journal of Computer-Aided Molecular Design, Vol.30 No.11, pp.1087-1100	DOI
2017-01	Absolute binding free energies for octa-acids and guests in SAMPL5 Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge Tofoleanu, Florentina; Lee, Ju Yong; Pickard, Frank C.; Koenig, Gerhard; Huang, Jing; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R. Journal of Computer-Aided Molecular Design, Vol.31 No.1, pp.107-118	DOI
2017-01	Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge Lee, Ju Yong; Tofoleanu, Florentina; Pickard, Frank C.; Konig, Gerhard; Huang, Jing; Damjanovic, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R. Journal of Computer-Aided Molecular Design, Vol.31 No.1, pp.71-85	DOI
2017-04	Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water Wu, Xiongwu; Lee, Ju Yong; Brooks, Bernard R. The Journal of Physical Chemistry B, Vol.121 No.15, pp.3318-3330	DOI
2017-05	Protein Loop Structure Prediction Using Conformational Space Annealing Heo, Seung Ryong; Lee, Ju Yong; Joo, Kee Hyoung; Shin, Hang Cheol; Lee, Joo Young Journal of Chemical Information and Modeling, Vol.57 No.5, pp.1068-1078	DOI
2017-05	Finding multiple reaction pathways via global optimization of action Lee, Ju Yong; Lee, In Ho; Joung, In Suk; Lee, Joo Young; Brooks, Bernard R. Nature Communications, Vol.8, p. 15443	DOI
2017-09	Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise Lee, Ju Yong; Zhang, Zhong Yuan; Lee, Joo Young; Brooks, Bernard R.; Ahn, Yong-Yeol Scientific Reports, Vol.7, p. 12399	DOI
2017-09	Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins Lee, Ju Yong; Konc, Janez; Janezic, Dusanka; Brooks, Bernard R. Scientific Reports, Vol.7, p. 11652	DOI
2019-06	Exploring the Folding Mechanism of Small Proteins GB1 and LB1 Cheng, Qianyi; Joung, InSuk; Lee, Ju Yong; Kuwajima, Kunihiro; Lee, Joo Young Journal of Chemical Theory and Computation, Vol.15 No.6, pp.3432-3449	DOI
2019-07	Cumulative directional calcium gluing between phosphate and silicate: A facile, robust and biocompatible strategy for siRNA delivery by amine-free non-positive vector Choi, Eun Shil; Lee, Ju Yong; Kwon, Ick Chan; Lim, Dong Kwon; Kim, Se Hoon Biomaterials, Vol.209, pp.126-137	DOI
2019-09	Assessment of network module identification across complex diseases Choobdar, Sarvenaz; Ahsen, Mehmet E.; Crawford, Jake; Tomasoni, Mattia; Fang, Tao; Lamparter, David; Lin, Junyuan; Hescott, Benjamin; Hu, Xiaozhe; Mercer, Johnathan; Natoli, Ted; Narayan, Rajiv; Aicheler, Fabian; Amoroso, Nicola; Arenas, Alex; Azhagesan, Karthik; Baker, Aaron; Banf, Michael; Batzoglou, Serafim; Baudot, Anais; Bellotti, Roberto; Bergmann, Sven; Boroevich, Keith A.; Brun, Christine; Cai, Stanley; Caldera, Michael; Calderone, Alberto; Cesareni, Gianni; Chen, Weiqi; Chichester, Christine; Cowen, Lenore; Cui, Hongzhu; Phuong Dao; De Domenico, Manlio; Dhroso, Andi; Didier, Gilles; Divine, Mathew; del Sol, Antonio; Feng, Xuyang; Flores-Canales, Jose C.; Fortunato, Santo; Gitter, Anthony; Gorska, Anna; Guan, Yuanfang; Guenoche, Alain; Gomez, Sergio; Hamza, Hatem; Hartmann, Andras; He, Shan; Heijs, Anton; Heinrich, Julian; Hu, Ying; Huang, Xiaoqing; Hughitt, V. Keith; Jeon, Minji; Jeub, Lucas; Johnson, Nathan T.; Joo, Keehyoung; Joung, InSuk; Jung, Sascha; Kalko, Susana G.; Kamola, Piotr J.; Kang, Jaewoo; Kaveelerdpotjana, Benjapun; Kim, Minjun; Kim, Yoo-Ah; Kohlbacher, Oliver; Korkin, Dmitry; Krzysztof, Kiryluk; Kunji, Khalid; Kutalik, Zoltan; Lage, Kasper; Lang-Brown, Sean; Thuc Duy Le; Lee, Jooyoung; Lee, Sunwon; Lee, Ju Yong; Li, Dong; Li, Jiuyong; Liu, Lin; Loizou, Antonis; Luo, Zhenhua; Lysenko, Artem; Ma, Tianle; Mall, Raghvendra; Marbach, Daniel; Mattia, Tomasoni; Medvedovic, Mario; Menche, Jorg; Micarelli, Elisa; Monaco, Alfonso; Mueller, Felix; Narykov, Oleksandr; Norman, Thea; Park, Sungjoon; Perfetto, Livia; Perrin, Dimitri; Pirro, Stefano; Przytycka, Teresa M.; Qian, Xiaoning; Raman, Karthik; Ramazzotti, Daniele; Ramsahai, Emilie; Ravindran, Balaraman; Rennert, Philip; Saez-Rodriguez, Julio; Scharfe, Charlotta; Sharan, Roded; Shi, Ning; Shin, Wonho; Shu, Hai; Sinha, Himanshu; Slonim, Donna K.; Spinelli, Lionel; Srinivasan, Suhas; Subramanian, Aravind; Suver, Christine; Szklarczyk, Damian; Tangaro, Sabina; Thiagarajan, Suresh; Tichit, Laurent; Tiede, Thorsten; Tripathi, Beethika; Tsherniak, Aviad; Tsunoda, Tatsuhiko; Turei, Denes; Ullah, Ehsan; Vahedi, Golnaz; Valdeolivas, Alberto; Vivek, Jayaswal; von Mering, Christian; Waagmeester, Andra; Wang, Bo; Wang, Yijie; Weir, Barbara A.; White, Shana; Winkler, Sebastian; Xu, Ke; Xu, Taosheng; Yan, Chunhua; Yang, Liuqing; Yu, Kaixian; Yu, Xiangtian; Zaffaroni, Gaia; Zaslavskiy, Mikhail; Zeng, Tao; Zhang, Jitao D.; Zhang, Lu; Zhang, Weijia; Zhang, Lixia; Zhang, Xinyu; Zhang, Junpeng; Zhou, Xin; Zhou, Jiarui; Zhu, Hongtu; Zhu, Junjie; Zuccon, Guido; Stolovitzky, Gustavo; Kutalik, Zoltan; Lage, Kasper; Slonim, Donna K.; Saez-Rodriguez, Julio; Cowen, Lenore J.; Bergmann, Sven; Marbach, Daniel Nature Methods, Vol.16 No.9, pp.843-+	DOI
2020-07	Direct global optimization of Onsager-Machlup action using Action-CSA Lee, Ju Yong; Brooks, Bernard R. Chemical Physics, Vol.535, p. 110768	DOI
2020-11	AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks Kwon, Yong Beom; Shin, Woong Hee; Ko, Jun Su; Lee, Ju Yong International Journal of Molecular Sciences, Vol.21 No.22, p. 8424	DOI
2020-12	Prediction of Molecular Electronic Transitions Using Random Forests Kang, Beomchang; Seok, Chaok; Lee, Ju Yong Journal of Chemical Information and Modeling, Vol.60 No.12, pp.5984-5994	DOI
2021-01	Substructure-based neural machine translation for retrosynthetic prediction Ucak, Umit V.; Kang, Taek; Ko, Jun Su; Lee, Ju Yong Journal of Cheminformatics, Vol.13 No.1, p. 4	DOI
2021-03	MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES Kwon, Yong Beom; Lee, Ju Yong Journal of Cheminformatics, Vol.13 No.1, p. 24	DOI
2021-10	MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization Kang, Beomchang; Seok, Chaok; Lee, Ju Yong ACS Omega, Vol.6 No.41, pp.27454-27465	DOI
2021-11	V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization Choi, Ji Eun; Lee, Ju Yong International Journal of Molecular Sciences, Vol.22 No.21, p. 11635	DOI
2022-01	Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields Byun, Jin Young; Lee, Ju Yong Life, Vol.12 No.1, p. 54	DOI
2022-03	A benchmark study of machine learning methods for molecular electronic transition: Tree-based ensemble learning versus graph neural network Kang, Beomchang; Seok, Chaok; Lee, Ju Yong Bulletin of the Korean Chemical Society, Vol.43 No.3, pp.328-335	DOI
2022-03	Retrosynthetic reaction pathway prediction through neural machine translation of atomic environments Ucak, Umit, V; Ashyrmamatov, Islambek; Ko, Jun Su; Lee, Ju Yong Nature Communications, Vol.13 No.1, p. 1186	DOI
2022-03	A-Prot: protein structure modeling using MSA transformer Hong, Yiyu; Lee, Ju Yong; Ko, Jun Su BMC Bioinformatics, Vol.23 No.1, p. 93	DOI
2022-04	Protein pKa Prediction by Tree-Based Machine Learning Chen, Ada Y.; Lee, Ju Yong; Damjanovic, Ana; Brooks, Bernard R. Journal of Chemical Theory and Computation, Vol.18 No.4, pp.2673-2686	DOI
2022-06	Cytosolic microRNA-inducible nuclear translocation of Cas9 protein for disease-specific genome modification Shin, Cheol Hee; Park, Su Chan; Park, Il Geun; Kim, Hyerim; An, Byoung Ha; Lee, Choongil; Kim, Sang Heon; Lee, Ju Yong; Lee, Ji Min; Oh, Seung Ja Nucleic Acids Research, Vol.50 No.10, pp.5919-5933	DOI
2022-06	CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields Lee, Sung Jong; Joo, Kee Hyoung; Sim, Sang Jin; Lee, Ju Yong; Lee, In Ho; Lee, Joo Young Molecules, Vol.27 No.12, p. 3711	DOI
2022-06	Discovery of penta-peptides inhibiting activity of formylglycine generating enzyme and its potential antibacterial effect against Mycobacterium tuberculosis Asiimwe, Nicholas; Al Mazid, Mohammad Faysal; Jeong, Yong Taek; Lee, Ju Yong; Lee, Jun Seok RSC Advances, Vol.12 No.29, pp.18884-18888	DOI
2022-08	S-Pred: protein structural property prediction using MSA transformer Hong, Yi Yu; Song, Jinung; Ko, Jun Su; Lee, Ju Yong; Shin, Woong Hee Scientific Reports, Vol.12 No.1, p. 13891	DOI
2023-01	Ligand-based pharmacophore modelling in search of novel anaplastic lymphoma kinase inhibitors Gajulapalli, V. Pratap Reddy; Lee, Ju Yong; Sohn, In Suk Results in Chemistry, Vol.5, p. 100752	DOI
2023-02	N4-phenylquinazoline-4,6-diamine as a tunable fluorescent scaffold for the development of fluorescent probes Lee, Jae Seok; Choi, Sang Kee; Aslam, Adil S.; Lim, Woo Jeong; Lee, Ju Yong; Ko, Jun Su; Ryu, Chan Hee; Lee, Kang Mun; Jung, Young Mee; Yoo, Hyuk Sang; Park, Ju Hyun; Lee, Sang Hee; Choi, Jun Won; Kim, Eun Ha; Park, Jong Min Dyes and Pigments, Vol.210, p. 110987	DOI
2023-02	Reconstruction of lossless molecular representations from fingerprints Ucak, Umit V. V.; Ashyrmamatov, Islambek; Lee, Ju Yong Journal of Cheminformatics, Vol.15 No.1, p. 13321	DOI
2023-02	Efficient discovery of multiple minimum action pathways using Gaussian process Shim, Jae Hwan; Lee, Ju Yong; Yu, Jae Jun Journal of Physics Communications, Vol.7 No.2, p. 025004	DOI
2023-05	Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization Ucak, Umit V. V.; Ashyrmamatov, Islambek; Lee, Ju Yong Journal of Cheminformatics, Vol.15 No.1, p. 55	DOI
2023-06	Characterization of the role of Kunitz-type protease inhibitor domain in dimerization of amyloid precursor protein Byun, Jin Young; Vellampatti, Srivithya; Chatterjee, Prathit; Hwang, Sun Ha; Kim, Byoung Choul; Lee, Ju Yong Journal of Computational Chemistry, Vol.44 No.15, pp.1437-1445	DOI
2023-10	Aβ dissociation by pectolinarin may counteract against Aβ-induced synaptic dysfunction and memory impairment Yi, Jee Hyun; Cho, Eun Bi; Lee, Soo Won; Kwon, Kyoung Ja; Lee, Seung Heon; Lee, Ju Yong; Lee, Chang Yeol; Shin, Chan Young; Kim, Dong Hyun; Shim, Sang Hee Biochemical Pharmacology, Vol.216, p. 115792	DOI
2024-02	Discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for treating cancers with microsatellite instability Yang, Hwa Sun; Kang, Mi So; Jang, Seon Yeong; Baek, Soo Yeon; Kim, Ji Won; Kim, Gyeong Un; Kim, Dong Woo; Ha, Jun Su; Kim, Jong Seung; Jung, Cheul Hee; Kim, Nam Jung; Cho, Sung Yup; Shin, Woong Hee; Lee, Ju Yong; Ko, Jun Su; Lee, An Soo; Keum, Gyo Chang; Lee, Sang Hee; Kang, Taek Bioorganic & Medicinal Chemistry, Vol.100, p. 117588	DOI