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Yong Duan - Publications

Affiliations: 
Applied Science Engineering University of California, Davis, Davis, CA 
Area:
General Biophysics, Computer Science, Biochemistry
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61 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
2017 Wang T, Liu H, Duan Y. Assessment of the transmembrane domain structures in GPCR Dock 2013 models. Journal of Structural Biology. PMID 29174398 DOI: 10.1016/J.Jsb.2017.11.007  0.535
2017 Wang T, Wang Y, Tang L, Duan Y, Liu H. 7x7 RMSD Matrix: A New Method for Quantitative Comparison of the Transmembrane Domain Structures in the G-protein Coupled Receptors. Journal of Structural Biology. PMID 28223044 DOI: 10.1016/J.Jsb.2017.02.005  0.55
2016 Liu H, Pei J, He Y, Lan X, Sun R, Deng T, Xu Y, Zhu G, Wang W, Duan Y, Ma H, Wang S, Fan J, Li C. Comparison of functional change in parotid gland after surgical excision of pleomorphic adenoma by two different types of parotidectomy. Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology. PMID 27492567 DOI: 10.1016/j.oooo.2016.03.023  0.463
2016 Duan Y, Yang Y, Wang Y, Liu H, Hong Y, Gong Q, Song Y. Comparison of anterior cervical discectomy and fusion with the zero-profile device versus plate and cage in treating cervical degenerative disc disease: A meta-analysis. Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia. PMID 27443497 DOI: 10.1016/j.jocn.2016.01.046  0.468
2016 Duan Y, Liu L, Han G, Liu H, Yu W, Yang G, Wang H, Wang H, Liu Y, Zahid, Waheed H. Anomalous behaviors of Wyrtki Jets in the equatorial Indian Ocean during 2013. Scientific Reports. 6: 29688. PMID 27436723 DOI: 10.1038/srep29688  0.467
2016 Duan Y, Qin L, Liu H. Different evolutionary pathways from B4 to B1 phase in AlN and InN: metadynamics investigations. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 205403. PMID 27120439 DOI: 10.1088/0953-8984/28/20/205403  0.486
2016 Zheng YC, Wang LZ, Zhao LJ, Zhao LJ, Zhan QN, Ma JL, Zhang B, Wang MM, Wang ZR, Li JF, Liu Y, Chen ZS, Shen DD, Liu XQ, Ren M, ... ... Duan YC, et al. 1,2,3-Triazole-Dithiocarbamate Hybrids, a Group of Novel Cell Active SIRT1 Inhibitors. Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology. 38: 185-193. PMID 26784898 DOI: 10.1159/000438620  0.481
2015 Fa Y, Liang W, Cui H, Duan Y, Yang M, Gao J, Liu H. Capillary ion chromatography-mass spectrometry for simultaneous determination of glucosylglycerol and sucrose in intracellular extracts of cyanobacteria. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1001: 169-73. PMID 26279008 DOI: 10.1016/j.jchromb.2015.07.054  0.464
2015 Zhang J, Duan Y, Jin Z, Wei Y, Yang S, Luo J, Ma D, Jing L, Liu H. Stent boost subtract imaging for the assessment of optimal stent deployment in coronary ostial lesion intervention: comparison with intravascular ultrasound. International Heart Journal. 56: 37-42. PMID 25742941 DOI: 10.1536/ihj.14-169  0.456
2015 Duan Y, Li F, Tan K, Liu H, Li Y, Liu Y, Kong X, Tang Y, Wu G, Yin Y. Key mediators of intracellular amino acids signaling to mTORC1 activation. Amino Acids. 47: 857-67. PMID 25701492 DOI: 10.1007/S00726-015-1937-X  0.489
2015 Yu M, Liu H, Duan Y, Zhang D, Li S, Wang F. Four types of fatty acids exert differential impact on pancreatic cancer growth. Cancer Letters. 360: 187-94. PMID 25676690 DOI: 10.1016/j.canlet.2015.02.002  0.484
2015 Zhu CY, Zheng FL, She XS, Zhao D, Gu Y, Duan YT, Chang AK, Liu HS. Identification of NS1 domains of avian H5N1 influenza virus which influence the interaction with the NOLC1 protein. Virus Genes. 50: 238-44. PMID 25645906 DOI: 10.1007/s11262-015-1166-0  0.501
2015 Duan Y, Li F, Liu H, Li Y, Liu Y, Kong X, Zhang Y, Deng D, Tang Y, Feng Z, Wu G, Yin Y. Nutritional and regulatory roles of leucine in muscle growth and fat reduction. Frontiers in Bioscience (Landmark Edition). 20: 796-813. PMID 25553480 DOI: 10.2741/4338  0.504
2014 Lei H, Sun J, Baldwin EP, Segal DJ, Duan Y. Conformational elasticity can facilitate TALE-DNA recognition. Advances in Protein Chemistry and Structural Biology. 94: 347-64. PMID 24629191 DOI: 10.1016/B978-0-12-800168-4.00009-3  0.311
2013 Zheng YC, Duan YC, Ma JL, Xu RM, Zi X, Lv WL, Wang MM, Ye XW, Zhu S, Mobley D, Zhu YY, Wang JW, Li JF, Wang ZR, Zhao W, et al. Triazole-dithiocarbamate based selective lysine specific demethylase 1 (LSD1) inactivators inhibit gastric cancer cell growth, invasion, and migration. Journal of Medicinal Chemistry. 56: 8543-60. PMID 24131029 DOI: 10.1021/Jm401002R  0.488
2013 Huang Y, Bu N, Duan Y, Pan Y, Liu H, Yin Z, Xiong Y. Electrohydrodynamic direct-writing. Nanoscale. 5: 12007-17. PMID 24057297 DOI: 10.1039/c3nr04329k  0.47
2013 Liu GZ, Xu HW, Wang P, Lin ZT, Duan YC, Zheng JX, Liu HM. Stereoselective synthesis and anti-proliferative effects on prostate cancer evaluation of 5-substituted-3,4-diphenylfuran-2-ones. European Journal of Medicinal Chemistry. 65: 323-36. PMID 23735281 DOI: 10.1016/j.ejmech.2013.04.062  0.485
2013 Duan YC, Zheng YC, Li XC, Wang MM, Ye XW, Guan YY, Liu GZ, Zheng JX, Liu HM. Design, synthesis and antiproliferative activity studies of novel 1,2,3-triazole-dithiocarbamate-urea hybrids. European Journal of Medicinal Chemistry. 64: 99-110. PMID 23644193 DOI: 10.1016/j.ejmech.2013.03.058  0.493
2013 Li K, Lin T, Zhang C, Fan X, Xu K, Bi L, Han J, Huang H, Liu H, Dong W, Duan Y, Yu M, Huang J. Optimal frequency of shock wave lithotripsy in urolithiasis treatment: a systematic review and meta-analysis of randomized controlled trials. The Journal of Urology. 190: 1260-7. PMID 23538240 DOI: 10.1016/j.juro.2013.03.075  0.456
2013 Duan YC, Ma YC, Zhang E, Shi XJ, Wang MM, Ye XW, Liu HM. Design and synthesis of novel 1,2,3-triazole-dithiocarbamate hybrids as potential anticancer agents. European Journal of Medicinal Chemistry. 62: 11-9. PMID 23353743 DOI: 10.1016/j.ejmech.2012.12.046  0.49
2013 Zhang Q, Lin L, Lu Y, Liu H, Duan Y, Zhu X, Zou C, Manning RD, Liu R. Interaction between nitric oxide and superoxide in the macula densa in aldosterone-induced alterations of tubuloglomerular feedback. American Journal of Physiology. Renal Physiology. 304: F326-32. PMID 23220724 DOI: 10.1152/ajprenal.00501.2012  0.482
2013 Zhu C, Zheng F, Sun T, Duan Y, Cao J, Feng H, Shang L, Zhu Y, Liu H. Interaction of avian influenza virus NS1 protein and nucleolar and coiled-body phosphoprotein 1. Virus Genes. 46: 287-92. PMID 23188192 DOI: 10.1007/s11262-012-0849-z  0.506
2012 Yuan YL, Wang YM, Liu H, Qin GF, Tang AG, Duan Y. Aberrant expression of E-cadherin in lung tissues of patients with probable lung cancer. Asian Pacific Journal of Cancer Prevention : Apjcp. 13: 5149-53. PMID 23244126  0.467
2012 Duan Y, Xing Z, Diao Z, Xu W, Li S, Du X, Wu G, Wang C, Lan T, Meng Z, Liu H, Wang F, Wu W, Xue Y. Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.). Plant Molecular Biology. 80: 429-42. PMID 22933119 DOI: 10.1007/s11103-012-9958-2  0.492
2012 Liu H, Duan Y, Jia Y, Gu Y, Li J, Yan C, Yang G. On-line simultaneous deproteinization of biological samples and trace enrichment of three dipine series using a poly(N-isopropylacrylamide-co-ethyleneglycol dimethacrylate) monolith. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 889: 55-60. PMID 22349122 DOI: 10.1016/j.jchromb.2012.01.030  0.473
2011 Katz MB, Graham GW, Duan Y, Liu H, Adamo C, Schlom DG, Pan X. Self-regeneration of Pd-LaFeO3 catalysts: new insight from atomic-resolution electron microscopy. Journal of the American Chemical Society. 133: 18090-3. PMID 22007950 DOI: 10.1021/Ja2082284  0.459
2011 Cui Y, Liu H, Zhou M, Duan Y, Li N, Gong X, Hu R, Hong M, Hong F. Signaling pathway of inflammatory responses in the mouse liver caused by TiO2 nanoparticles. Journal of Biomedical Materials Research. Part A. 96: 221-9. PMID 21105171 DOI: 10.1002/jbm.a.32976  0.489
2010 Duan Y, Diao Z, Liu H, Cai M, Wang F, Lan T, Wu W. Molecular cloning and functional characterization of OsJAG gene based on a complete-deletion mutant in rice (Oryza sativa L.). Plant Molecular Biology. 74: 605-15. PMID 20938801 DOI: 10.1007/s11103-010-9703-7  0.487
2010 Cui Y, Gong X, Duan Y, Li N, Hu R, Liu H, Hong M, Zhou M, Wang L, Wang H, Hong F. Hepatocyte apoptosis and its molecular mechanisms in mice caused by titanium dioxide nanoparticles. Journal of Hazardous Materials. 183: 874-80. PMID 20724067 DOI: 10.1016/j.jhazmat.2010.07.109  0.502
2010 Li N, Duan Y, Hong M, Zheng L, Fei M, Zhao X, Wang J, Cui Y, Liu H, Cai J, Gong S, Wang H, Hong F. Spleen injury and apoptotic pathway in mice caused by titanium dioxide nanoparticules. Toxicology Letters. 195: 161-8. PMID 20381595 DOI: 10.1016/j.toxlet.2010.03.1116  0.509
2010 Duan Y, Liu J, Ma L, Li N, Liu H, Wang J, Zheng L, Liu C, Wang X, Zhao X, Yan J, Wang S, Wang H, Zhang X, Hong F. Toxicological characteristics of nanoparticulate anatase titanium dioxide in mice. Biomaterials. 31: 894-9. PMID 19857890 DOI: 10.1016/J.Biomaterials.2009.10.003  0.482
2010 Duan Y, Li N, Liu C, Liu H, Cui Y, Wang H, Hong F. Interaction between nanoparticulate anatase TiO2 and lactate dehydrogenase. Biological Trace Element Research. 136: 302-13. PMID 19841870 DOI: 10.1007/s12011-009-8548-x  0.516
2010 Ma L, Liu J, Li N, Wang J, Duan Y, Yan J, Liu H, Wang H, Hong F. Oxidative stress in the brain of mice caused by translocated nanoparticulate TiO2 delivered to the abdominal cavity. Biomaterials. 31: 99-105. PMID 19783296 DOI: 10.1016/J.Biomaterials.2009.09.028  0.483
2009 Li N, Ma L, Wang J, Zheng L, Liu J, Duan Y, Liu H, Zhao X, Wang S, Wang H, Hong F, Xie Y. Interaction Between Nano-Anatase TiO(2) and Liver DNA from Mice In Vivo. Nanoscale Research Letters. 5: 108-115. PMID 20652136 DOI: 10.1007/S11671-009-9451-2  0.492
2009 Xu LL, Liu HC, Wang DS, E LL, Xu L, Jin ZL, Duan YZ. Effects of BMP-2 and dexamethasone on osteogenic differentiation of rat dental follicle progenitor cells seeded on three-dimensional beta-TCP. Biomedical Materials (Bristol, England). 4: 065010. PMID 19966384 DOI: 10.1088/1748-6041/4/6/065010  0.47
2009 Lei H, Wang ZX, Wu C, Duan Y. Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations. The Journal of Chemical Physics. 131: 165105. PMID 19894980 DOI: 10.1063/1.3238567  0.306
2009 Ma L, Ze Y, Liu J, Liu H, Liu C, Li Z, Zhao J, Yan J, Duan Y, Xie Y, Hong F. Direct evidence for interaction between nano-anatase and superoxide dismutase from rat erythrocytes. Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy. 73: 330-5. PMID 19345606 DOI: 10.1016/J.Saa.2009.02.041  0.517
2009 Duan Y, Liu H, Zhao J, Liu C, Li Z, Yan J, Ma L, Liu J, Xie Y, Ruan J, Hong F. The effects of nano-anatase TiO(2) on the activation of lactate dehydrogenase from rat heart. Biological Trace Element Research. 130: 162-71. PMID 19214398 DOI: 10.1007/s12011-009-8326-9  0.512
2008 Lei H, Deng X, Wang Z, Duan Y. The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier. The Journal of Chemical Physics. 129: 155104. PMID 19045234 DOI: 10.1063/1.2995987  0.306
2008 Lei H, Wu C, Wang ZX, Zhou Y, Duan Y. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. The Journal of Chemical Physics. 128: 235105. PMID 18570534 DOI: 10.1063/1.2937135  0.337
2008 Lei H, Duan Y. Protein folding and unfolding by all-atom molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 443: 277-95. PMID 18446293 DOI: 10.1007/978-1-59745-177-2_15  0.3
2008 Liu H, Dastidar SG, Lei H, Zhang W, Lee MC, Duan Y. Conformational changes in protein function. Methods in Molecular Biology (Clifton, N.J.). 443: 258-75. PMID 18446292 DOI: 10.1007/978-1-59745-177-2_14  0.573
2008 Liu H, Duan Y. Effects of posttranslational modifications on the structure and dynamics of histone H3 N-terminal Peptide. Biophysical Journal. 94: 4579-85. PMID 18192367 DOI: 10.1529/Biophysj.107.115824  0.548
2007 Lei H, Duan Y. Two-stage folding of HP-35 from ab initio simulations. Journal of Molecular Biology. 370: 196-206. PMID 17512537 DOI: 10.1016/J.Jmb.2007.04.040  0.316
2007 Wang T, Duan Y. Chromophore channeling in the G-protein coupled receptor rhodopsin. Journal of the American Chemical Society. 129: 6970-1. PMID 17500517 DOI: 10.1021/Ja0691977  0.301
2007 Lei H, Wu C, Liu H, Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 104: 4925-30. PMID 17360390 DOI: 10.1073/Pnas.0608432104  0.569
2006 Lei H, Dastidar SG, Duan Y. Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations. The Journal of Physical Chemistry. B. 110: 22001-8. PMID 17064170 DOI: 10.1021/Jp063716A  0.31
2006 Zhang W, Duan Y. Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement. Protein Engineering, Design & Selection : Peds. 19: 55-65. PMID 16401632 DOI: 10.1093/Protein/Gzj001  0.316
2005 Chowdhury S, Lei H, Duan Y. Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A. The Journal of Physical Chemistry. B. 109: 9073-81. PMID 16852080 DOI: 10.1021/Jp0449814  0.311
2005 Zhang W, Wu C, Duan Y. Convergence of replica exchange molecular dynamics. The Journal of Chemical Physics. 123: 154105. PMID 16252940 DOI: 10.1063/1.2056540  0.305
2005 Sarakatsannis JN, Duan Y. Statistical characterization of salt bridges in proteins. Proteins. 60: 732-9. PMID 16021620 DOI: 10.1002/Prot.20549  0.303
2005 Lee MC, Deng J, Briggs JM, Duan Y. Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. Biophysical Journal. 88: 3133-46. PMID 15731379 DOI: 10.1529/Biophysj.104.058446  0.315
2004 Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins. 55: 620-34. PMID 15103626 DOI: 10.1002/Prot.10470  0.312
2004 Chowdhury S, Lee aMC, Duan Y. Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations Journal of Physical Chemistry B. 108: 13855-13865. DOI: 10.1021/Jp0478920  0.328
2003 Chowdhury S, Lee MC, Xiong G, Duan Y. Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution Journal of Molecular Biology. 327: 711-717. PMID 12634063 DOI: 10.1016/S0022-2836(03)00177-3  0.325
2003 Chowdhury S, Zhang W, Wu C, Xiong G, Duan Y. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers. 68: 63-75. PMID 12579580 DOI: 10.1002/Bip.10216  0.304
2000 Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research. 33: 889-97. PMID 11123888 DOI: 10.1021/Ar000033J  0.314
2000 Lee MR, Duan Y, Kollman PA. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins. 39: 309-16. PMID 10813813 DOI: 10.1002/(Sici)1097-0134(20000601)39:4<309::Aid-Prot40>3.0.Co;2-S  0.31
1999 Wang L, Duan Y, Shortle R, Imperiali B, Kollman PA. Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures. Protein Science : a Publication of the Protein Society. 8: 1292-304. PMID 10386879 DOI: 10.1110/Ps.8.6.1292  0.325
1998 Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science (New York, N.Y.). 282: 740-4. PMID 9784131 DOI: 10.1126/Science.282.5389.740  0.319
1998 Duan Y, Wang L, Kollman PA. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. 95: 9897-902. PMID 9707572 DOI: 10.1073/Pnas.95.17.9897  0.322
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