Publications
Xu D*, Caylor ML, Rahman S, Huang Y, Tao A, Shinohara Y. ezFAERS: Deep FAERS Drug Data Standardization and Encoding 2020.
Xu D*, Caylor ML, Rahman S, Huang Y, Tao A, Shinohara Y. ezFAERS: Deep FAERS Drug Data Standardization and Encoding 2020.
Cornell KA, Knippel R, Cortright G, Fonken M, Guerrero C, Hall A, Mitchell K, Thurston J, Erstad P, Tao A, Xu D. Characterization of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidases from Borrelia burgdorferi: Antibiotic Targets for Lyme Disease. BBA - General Subjects, 1864(1), 129455, 2020. 10.1016/j.bbagen.2019.129455
Cornell KA, Knippel R, Cortright G, Fonken M, Guerrero C, Hall A, Mitchell K, Thurston J, Erstad P, Tao A, Xu D. Characterization of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidases from Borrelia burgdorferi: Antibiotic Targets for Lyme Disease. BBA - General Subjects, 1864(1), 129455, 2020. 10.1016/j.bbagen.2019.129455
Culbertson VL, Rahman S, Bosen GC, Caylor ML, Xu D*. Use of a Bioinformatics-Based Toxicity Scoring System to Assess Serotonin Burden and Predict Population-Level Adverse Drug Events from Concomitant Serotonergic Drug Therapy, Pharmacotherapy, 39(2):171–181, 2019. 10.1002/phar.2215.
Culbertson VL, Rahman S, Bosen GC, Caylor ML, Xu D*. Use of a Bioinformatics-Based Toxicity Scoring System to Assess Serotonin Burden and Predict Population-Level Adverse Drug Events from Concomitant Serotonergic Drug Therapy, Pharmacotherapy, 39(2):171–181, 2019. 10.1002/phar.2215.
Tao A, Huang Y, Shinohara Y, Caylor ML, Pashikanti S, Xu D*. ezCADD: A Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. Journal of Chemical Information and Modeling, 59, 1, 18-24, 2019. 10.1021/acs.jcim.8b00633
Tao A, Huang Y, Shinohara Y, Caylor ML, Pashikanti S, Xu D*. ezCADD: A Rapid 2D/3D Visualization Enabled Web Modeling Environment for Democratizing Computer-Aided Drug Design. Journal of Chemical Information and Modeling, 59, 1, 18-24, 2019. 10.1021/acs.jcim.8b00633
Culbertson VL, Rahman S, Bosen GC, Caylor ML, Echevarria MM, Xu D*, Implications of Off-Target Serotonergic Drug Effects - A Bioinformatics Molecular Analysis of Serotonin Syndrome Reports. Pharmacotherapy, 38(9), 888–898, 2018. 10.1002/phar.2163
Culbertson VL, Rahman S, Bosen GC, Caylor ML, Echevarria MM, Xu D*, Implications of Off-Target Serotonergic Drug Effects - A Bioinformatics Molecular Analysis of Serotonin Syndrome Reports. Pharmacotherapy, 38(9), 888–898, 2018. 10.1002/phar.2163
Xu D*, Smolin N, Shaw RK, Battey SR, Tao A, Huang Y, Rahman S, Caylor ML. Molecular Insights into the Improved Clinical Performance of PEGylated Interferon Therapeutics: A Molecular Dynamics Perspective. RSC Advances, 8, 2315-2322, 2018. 10.1039/C7RA12480E
Xu D*, Smolin N, Shaw RK, Battey SR, Tao A, Huang Y, Rahman S, Caylor ML. Molecular Insights into the Improved Clinical Performance of PEGylated Interferon Therapeutics: A Molecular Dynamics Perspective. RSC Advances, 8, 2315-2322, 2018. 10.1039/C7RA12480E
Madaras-Kelly K, Remington R, Hruza H, Xu D. The Comparative Effectiveness of High-Dose Versus Standard-Dose Influenza Vaccines in Preventing Post-Influenza Deaths. Journal of Infectious Diseases, 218(20), 336–337, 2018. 10.1093/infdis/jix645
Madaras-Kelly K, Remington R, Hruza H, Xu D. The Comparative Effectiveness of High-Dose Versus Standard-Dose Influenza Vaccines in Preventing Post-Influenza Deaths. Journal of Infectious Diseases, 218(20), 336–337, 2018. 10.1093/infdis/jix645
Xu D*, Ham AG, Tivis RD, Caylor ML, Tao A, Flynn ST, Economen PJ, Dang HK, Johnson RW, Culbertson VL. MSBIS: A Multi-Step Biomedical Informatics Screening Approach for Identifying Medications that Mitigate the Risks of Metoclopramide-Induced Tardive Dyskinesia. EBioMedicine, 26, 132-137, 2017. 10.1016/j.ebiom.2017.11.015
Xu D*, Ham AG, Tivis RD, Caylor ML, Tao A, Flynn ST, Economen PJ, Dang HK, Johnson RW, Culbertson VL. MSBIS: A Multi-Step Biomedical Informatics Screening Approach for Identifying Medications that Mitigate the Risks of Metoclopramide-Induced Tardive Dyskinesia. EBioMedicine, 26, 132-137, 2017. 10.1016/j.ebiom.2017.11.015
Xu D*, Anderson HD, Tao A, Hannah KL, Linnebur SA, Valuck RJ, Culbertson VL. Assessing and Predicting Drug-Induced Anticholinergic Risks: An Integrated Computational Approach. Therapeutic Advances in Drug Safety, 8(11): 361-370, 2017. 10.1177/2042098617725267
Xu D*, Anderson HD, Tao A, Hannah KL, Linnebur SA, Valuck RJ, Culbertson VL. Assessing and Predicting Drug-Induced Anticholinergic Risks: An Integrated Computational Approach. Therapeutic Advances in Drug Safety, 8(11): 361-370, 2017. 10.1177/2042098617725267
Aldape MJ, Tao A, Heeney DD, McIndoo ER, French JM, Xu D*. Experimental Identification and Computational Characterization of a Novel Extracellular Metalloproteinase Produced by Clostridium sordellii. RSC Advances, 7, 13928-13938, 2017. 10.1039/C6RA27654G
Aldape MJ, Tao A, Heeney DD, McIndoo ER, French JM, Xu D*. Experimental Identification and Computational Characterization of a Novel Extracellular Metalloproteinase Produced by Clostridium sordellii. RSC Advances, 7, 13928-13938, 2017. 10.1039/C6RA27654G
Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. J. Chem. Theory Comput. 8(5): 1542–1555, 2012. 10.1021/ct200909j
Götz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. J. Chem. Theory Comput. 8(5): 1542–1555, 2012. 10.1021/ct200909j
Forbey JS, Pu X, Xu D, Kielland K, Bryant J. Inhibition of Snowshoe Hare Succinate Dehydrogenase Activity as a Mechanism of Deterrence for Papyriferic Acid in Birch. J. Chem. Ecol., 137(12):1285-1293, 2011. 10.1007/s10886-011-0039-9
Forbey JS, Pu X, Xu D, Kielland K, Bryant J. Inhibition of Snowshoe Hare Succinate Dehydrogenase Activity as a Mechanism of Deterrence for Papyriferic Acid in Birch. J. Chem. Ecol., 137(12):1285-1293, 2011. 10.1007/s10886-011-0039-9
Xu D, Williamson MJ, Walker RC. Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units. Annu. Rep. Comp. Chem., 6:113-324, 2010. 10.1016/S1574-1400(10)06001-9
Xu D, Williamson MJ, Walker RC. Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units. Annu. Rep. Comp. Chem., 6:113-324, 2010. 10.1016/S1574-1400(10)06001-9
Zou W, Xu D, Zajac P, Cooksy AL, Bersuker IB, Liu Y, Boggs JE. Symmetry Breaking in Linear ZnCl2+: A Theoretical Study. J. Mol., Struct. 978:263-268, 2010. 10.1016/j.molstruc.2010.03.082
Zou W, Xu D, Zajac P, Cooksy AL, Bersuker IB, Liu Y, Boggs JE. Symmetry Breaking in Linear ZnCl2+: A Theoretical Study. J. Mol., Struct. 978:263-268, 2010. 10.1016/j.molstruc.2010.03.082
Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PRL, McCammon JA, Li WW, Arzberger PW. Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective J. Mol. Biol., 387:465-491, 2009. 10.1016/j.jmb.2009.01.040
Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PRL, McCammon JA, Li WW, Arzberger PW. Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective J. Mol. Biol., 387:465-491, 2009. 10.1016/j.jmb.2009.01.040
Newhouse EI, Xu D, Amaro RE, Pao HC, Markwick PRL, Wu KJ, Alam M, McCammon JA, Li WW, Arzberger PW. Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective. J. Am. Chem. Soc., 131 (47):17430–17442, 2009. 10.1021/ja904052q
Newhouse EI, Xu D, Amaro RE, Pao HC, Markwick PRL, Wu KJ, Alam M, McCammon JA, Li WW, Arzberger PW. Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective. J. Am. Chem. Soc., 131 (47):17430–17442, 2009. 10.1021/ja904052q
Amaro RE, Cheng X, Ivanov I, Xu D, Mccammon JA. Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations. J. Am. Chem. Soc., 131 (13):4702–4709, 2009. 10.1021/ja8085643
Amaro RE, Cheng X, Ivanov I, Xu D, Mccammon JA. Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations. J. Am. Chem. Soc., 131 (13):4702–4709, 2009. 10.1021/ja8085643
Xu D, Stare J, Cooksy AL. Solving the Vibrational Schrodinger Equation on an Arbitrary Multidimensional Potential Energy Surface by the Finite Element Method. Comp. Phys. Comm., 180 (11):2079-209, 2009. 10.1016/j.cpc.2009.06.010
Xu D, Stare J, Cooksy AL. Solving the Vibrational Schrodinger Equation on an Arbitrary Multidimensional Potential Energy Surface by the Finite Element Method. Comp. Phys. Comm., 180 (11):2079-209, 2009. 10.1016/j.cpc.2009.06.010
Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase. J. Med. Chem., 51 (13): 3878–3894, 2008. 10.1021/jm8001197
Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA. Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase. J. Med. Chem., 51 (13): 3878–3894, 2008. 10.1021/jm8001197
Xu D, Redman-Furey N. Statistical Cluster Analysis of Pharmaceutical Solvents. Intl. J. Pharm., 339:175-188, 2007. 10.1016/j.ijpharm.2007.03.002
Xu D, Redman-Furey N. Statistical Cluster Analysis of Pharmaceutical Solvents. Intl. J. Pharm., 339:175-188, 2007. 10.1016/j.ijpharm.2007.03.002
Xu D, Cooksy AL. Ab Initio Study of the Torsional Motion in Tolane. J. Mol. Struct. THEOCHEM, 815:119-125, 2007. 10.1016/j.theochem.2007.03.028
Xu D, Cooksy AL. Ab Initio Study of the Torsional Motion in Tolane. J. Mol. Struct. THEOCHEM, 815:119-125, 2007. 10.1016/j.theochem.2007.03.028
Zhang K, Zhang H, Xua G, Xiang S, Xu D, Liu S, Li H. Alkylation of Phenol with Tert-butyl Alcohol Catalyzed by Large Pore Zeolites. Applied Catalysis A: General, 207:183-190, 2001. 10.1016/S0926-860X(00)00663-38
Zhang K, Zhang H, Xua G, Xiang S, Xu D, Liu S, Li H. Alkylation of Phenol with Tert-butyl Alcohol Catalyzed by Large Pore Zeolites. Applied Catalysis A: General, 207:183-190, 2001. 10.1016/S0926-860X(00)00663-38
Zhang K, Xu D, Huang C, Zhang H, Xiang S, Liu S, Li H. Alkylation of Phenol with Tert-butyl Alcohol Catalysed by Zeolite Hβ. Applied Catalysis A: General, 166:89-95, 1998. 10.1016/S0926-860X(97)00376-1
Zhang K, Xu D, Huang C, Zhang H, Xiang S, Liu S, Li H. Alkylation of Phenol with Tert-butyl Alcohol Catalysed by Zeolite Hβ. Applied Catalysis A: General, 166:89-95, 1998. 10.1016/S0926-860X(97)00376-1
