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Showing results 1 to 15 of 15

Issue Date	Title / Author(s) / Citation	File	Altmetrics
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
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
2016-11	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 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
2017-01	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
2017-04	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	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
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
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

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