Huan Rui, Ph.D. - Publications

2013 Biochemistry and Molecular Biology University of Kansas, Lawrence, KS, United States 

30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Barium blockade of the KcsA channel in open and closed conformation datasets. Data in Brief. 32: 106135. PMID 32904340 DOI: 10.1016/j.dib.2020.106135  0.68
2020 Rohaim A, Gong L, Li J, Rui H, Blachowicz L, Roux B. Open and closed structures of a barium-blocked potassium channel. Journal of Molecular Biology. PMID 32615129 DOI: 10.1016/j.jmb.2020.06.012  0.68
2019 Ellis-Guardiola K, Rui H, Beckner RL, Srivastava P, Sukumar N, Roux B, Lewis JC. Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase. Biochemistry. PMID 30786206 DOI: 10.1021/acs.biochem.9b00031  0.68
2018 Rui H, Das A, Nakamoto R, Roux B. Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. Journal of Molecular Biology. 430: 5050-5065. PMID 30539761 DOI: 10.1016/j.jmb.2018.10.014  0.68
2017 Li J, Ostmeyer J, Boulanger E, Rui H, Perozo E, Roux B. Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973956 DOI: 10.1073/pnas.1706983114  0.68
2017 Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophysical Journal. 112: 1185-1197. PMID 28355546 DOI: 10.1016/j.bpj.2017.01.028  1
2017 Das A, Rui H, Nakamoto R, Roux B. Conformational transitions and alternating-access mechanism in the sarcoplasmic reticulum calcium pump. Journal of Molecular Biology. PMID 28093226 DOI: 10.1016/j.jmb.2017.01.007  0.68
2016 Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/jcc.24660  1
2016 Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nature Communications. 7: 12753. PMID 27678077 DOI: 10.1038/ncomms12753  0.68
2016 Rui H, Artigas P, Roux B. The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion. Elife. 5. PMID 27490484 DOI: 10.7554/eLife.16616  0.68
2016 Li J, Rui H, Yu D. Trapezoidal Rule for Computing Supersingular Integral on a Circle Journal of Scientific Computing. 66: 740-760. DOI: 10.1007/s10915-015-0042-3  0.44
2015 Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M. Mechanism of potassium ion uptake by the Na(+)/K(+)-ATPase. Nature Communications. 6: 7622. PMID 26205423 DOI: 10.1038/ncomms8622  0.68
2015 Roux B, Rui H, Das A. 49 Structure and energetics of the pumping mechanism of membrane ATPase. Journal of Biomolecular Structure & Dynamics. 33: 33-4. PMID 26103258 DOI: 10.1080/07391102.2015.1032598  0.68
2015 He YC, Liu F, Gong L, Zhu ZZ, Ding Y, Wang C, Xue YF, Rui H, Tao ZC, Zhang DP, Ma CL. Significantly improving enzymatic saccharification of high crystallinity index's corn stover by combining ionic liquid [Bmim]Cl-HCl-water media with dilute NaOH pretreatment. Bioresource Technology. 189: 421-5. PMID 25921785 DOI: 10.1016/j.biortech.2015.04.047  0.44
2015 Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry. 54: 1611-27. PMID 25640193 DOI: 10.1021/bi501255r  1
2014 Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/bs.apcsb.2014.06.002  1
2014 Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/jcc.23702  1
2014 Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107: 134-45. PMID 24988348 DOI: 10.1016/j.bpj.2014.05.034  1
2014 Rui H, Root KT, Lee J, Glover KJ, Im W. Probing the U-shaped conformation of caveolin-1 in a bilayer. Biophysical Journal. 106: 1371-80. PMID 24655512 DOI: 10.1016/j.bpj.2014.02.005  1
2013 Zhao Q, Rui H, Li J. Superconvergence of Hermite rule for hypersingular integrals on interval International Journal of Computer Mathematics. DOI: 10.1080/00207160.2012.752076  0.44
2012 Rui H, Rivera M, Im W. Protein dynamics and ion traffic in bacterioferritin. Biochemistry. 51: 9900-10. PMID 23167635 DOI: 10.1021/bi3013388  1
2012 Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. Journal of Computational Chemistry. 33: 331-9. PMID 22102176 DOI: 10.1002/jcc.21952  1
2011 Rui H, Kumar R, Im W. Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating. Biophysical Journal. 101: 671-9. PMID 21806935 DOI: 10.1016/j.bpj.2011.06.029  1
2011 Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophysical Journal. 100: 611-9. PMID 21281575 DOI: 10.1016/j.bpj.2010.12.3708  1
2011 Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophysical Journal. 100: 602-10. PMID 21281574 DOI: 10.1016/j.bpj.2010.12.3711  1
2010 Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/jp108166k  1
2010 Rui H, Im W. Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. Journal of Computational Chemistry. 31: 2859-67. PMID 20589740 DOI: 10.1002/jcc.21580  1
2010 Jepkorir G, Rodríguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa. Journal of the American Chemical Society. 132: 9857-72. PMID 20572666 DOI: 10.1021/ja103498z  1
2009 Rui H, Lee J, Im W. Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers. Biophysical Journal. 97: 787-95. PMID 19651037 DOI: 10.1016/j.bpj.2009.05.029  1
2009 Im W, Lee J, Kim T, Rui H. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. Journal of Computational Chemistry. 30: 1622-33. PMID 19496166 DOI: 10.1002/jcc.21320  1
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