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Pang, Yuan-Ping (computer-aided molecular design)

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Publications

Click here to see Dr. Pang's complete list of publications.

  1. EUDOC on Blue Gene: Accelerating the Transfer of Drug Discoveries from Laboratory to Patient, Yuan-Ping Pang, Tim Mullins, Brent Swartz, Jeffrey McAllister, Brian Smith, Charles Archer, Roy Musselman, Amanda Peters, Brian Wallenfelt, Kurt Pinnow, IBM J. Res. Dev., 52, 69-81 (2008).
  2. Convenient Synthesis of a Library of Discrete Hydroxamic Acids Using the Hydroxythiophenol (Marshall) Resin. Jinil Choi, Jewn Giew Park, and Yuan-Ping Pang, Tetrahedron Lett., 49, 1103-1106 (2008).
  3. Normal-Mode-Analysis–Monitored Energy Minimization Procedure for Generating Small–Molecule Bound Conformations.. Qi Wang and Yuan-Ping Pang, PLoS ONE, 2(10): e1025. doi:10.1371/journal.pone.0001025 (2007).
  4. Preference of Small Molecules for Local Minimum Conformations When Binding to Proteins. Qi Wang and Yuan-Ping Pang, PLoS ONE, 2(9): e820. doi:10.1371/journal.pone.0000820 (2007).
  5. Computer-aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A. Jing Tang, Jewn Giew Park, Charles B. Millard, James J. Schmidt, and Yuan-Ping Pang, PLoS ONE, 2(8): e761. doi:10.1371/journal.pone.0000761 (2007).
  6. Accurate reproduction of 161 small-molecule crystal structures using the EUDOC program: expanding the use of EUDOC to supramolecular chemistry. Qi Wang and Yuan-Ping Pang, PLoS ONE, 2(6): e531. doi:10.1371/journal.pone.0000531 (2007).
  7. Novel Nerve-Agent Antidote Design Based on Crystallographic and Mass Spectrometric Analyses of Tabun-Conjugated Acetylcholinesterase in Complex with Antidotes. Fredrik J. Ekström, Crister Åstot, and Yuan-Ping Pang, Clinical Pharmacology & Therapeutics, 82, 282-293 (2007).
  8. Novel Acetylcholinesterase Target Site for Malaria Mosquito Control. Yuan-Ping Pang, PLoS ONE, 1(1): e58. doi:10.1371/journal.pone.0000058 (2006)
  9. In Silico Drug Discovery: Solving the “Target-Rich and Lead-Poor” Imbalance Using the Genome-to-Drug-Lead Paradigm, Yuan-Ping Pang, Clinical Pharmacology & Therapeutics, 81, 30-34 (2007).
  10. Species Marker for Developing Novel and Safe Pesticides, Yuan-Ping Pang, Bioorg. Med. Chem. Lett., 17, 197-199 (2007)
  11. Crystal Structures of Acetylcholinesterase in Complex with HI-6, Ortho-7 and Obidoxime: Structural Basis for Differences in the Ability to Reactivate Tabun Conjugates. Fredrik Ekström, Yuan-Ping Pang, Malin Boman, Elisabet Artursson, Christine Akfur, and Susanne Lundberg, Biochemical Pharmacology, 72, 597-607, (2006).
  12. Bis-Imidazoles as Molecular Probes for Peripheral Sites of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A. Isidro Merino, Jason D. Thompson, Charles B. Millard, James J. Schmidt, and Yuan-Ping Pang, Bioorg. Med. Chem., 14, 3583-3591 (2006).
  13. From genome to drug lead: Identification of a small-molecule inhibitor of the SARS virus. Andrea J. Dooley, Nice Shindo, Barbara Taggart, Jewn-Giew Park and Yuan-Ping Pang, Bioorg. Med. Chem. Lett., 16, 830-833 (2006).
  14. Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A. JG Park, PC Sill, EF Makiyi, AT Garcia-Sosa, CB Millard, JJ Schmidt, YP Pang, Bioorg. Med. Chem., 14, 395-408 (2006).
  15. A potent and Selective Tacrine Analog - Biomembrane Permeation and Physicochemical Characterization. George A. Patani, Yuan-Ping Pang, Yie W. Chien, Pharm. Dev. Technol., 10, 525-538 (2005).
  16. Novel dimeric acetylcholinesterase inhibitor bis(7)-tacrine, but not donepezil, prevents glutamate-induced neuronal apoptosis by blocking N-methyl-D-aspartate receptors. WM Li, RB Pi, HHN Chan, HJ Fu, NTK Lee, HW Tsang, YM Pu, DC Chang, CY Li, JL Luo, KM Xiong, ZW Li, H Xue, PR Carlier, YP Pang, KWK Tsim, MT Li, YF Han, J. Biol. Chem., 280, 18179-18188 (2005).
  17. Inhibition by bis(7)-tacrine of 5-HT-activated current in rat TG neurons. JL Luo, J Zhang, BC Guan, YP Pang, YF Han, ZW Li, Neuroreport, 15, 1335-1338 (2004).
  18. Nonbonded Bivalence Approach to Cell-Permeable Molecules That Target DNA Sequences. Yuan-Ping Pang, Bioorg. Med. Chem., 12, 3063-3068 (2004).
  19. Improved Loading and cleavage Methods for Solid-Phase Synthesis Using Chlorotrityl Resins: Synthesis and Testing of a Library of 144 Discrete Chemicals as Potential Farnesyltransferase Inhibitors. Jewn Giew Park, Kevin J. Langenwalter, Carolyn A. Weinbaum, Patrick J. Casey, Yuan-Ping Pang, J. Comb. Chem., 6, 407-413 (2004).
  20. Cholinesterase Reactivation in Vivo with a Novel Bis-Oxime Optimized by Computer-Aided Design. PI Hammond, C. Kern, F. Hong, TM Kollmeyer, Y-P Pang, and S Brimijoin, J. Pharmaco. Exp. Ther., 307, 190-196 (2003).
  21. Rational Design of Alkylene-Linked Bis-Pyridiniumaldoximes as Improved Acetylcholinesterase Reactivators. Yuan-Ping Pang, Thomas M. Kollmeyer, Feng Hong, Jong-Cheol Lee, Pamela I. Hammond, Sharie P. Haugabouk, and Stephen Brimijoin, Chem. Biol. 10, 491-502 (2003).
  22. Re-Engineering Butyrylcholinesterase as a Cocaine Hydrolase. Hong Sun, Yuan-Ping Pang, Oksana Lockridge, and Stephen Brimijoin, Mol. Pharmacol., 62, 220-224 (2002).
  23. Theoretical 3D Model of Histamine N-Methyltransferase: Insights into the Effects of a Genetic Polymorphism on Enzymatic Activity and Thermal Stability. Y.-P. Pang, X.-E. Zheng, and R. M. Weinshilboum, Biochem. Bioph. Res. Commun., 287, 204-208 (2001).
  24. Discovery of a New Inhibitor Lead of Adenovirus Proteinase: Steps Toward Selective, Irreversible Inhibitors of Cysteine Proteinases. Yuan-Ping Pang, Kun Xu, Thomas M. Kollmeyer, Emanuele Perola, William J. McGrath, Dave T. Green, and Walter F. Mangel, FEBS Lett., 502, 93-97 (2001).
  25. Successful Molecular Dynamics Simulation of Two Zinc Complexes Bridged by a Hydroxide in Phosphotriesterase Using the Cationic Dummy Atom Method. Yuan-Ping Pang, Proteins, 45, 183-189 (2001).
  26. EUDOC: A Computer Program for Identification of Drug Interaction Sites in Macromolecules and Drug Leads from Chemical Databases. Yuan-Ping Pang, Emanuele Perola, Kun Xu, and Franklyn G. Prendergast, J. Comp. Chem., 22, 1750-1771 (2001).
  27. Predicted Michaelis-Menten Complexes of Cocaine-Butyrylcholinesterase: Engineering Effective Butyrylcholinesterase Mutants for Cocaine Detoxication. Hong Sun, Jamal El Yazal, Oksana Lockridge, Lawrence M Schopfer, Stephen Brimijoin, and Yuan-Ping Pang, J. Biol. Chem., 276, 9330-9336 (2001).
  28. Protonation States of the Chromophore of Denatured Green Fluorescent Proteins Predicted by ab Initio Calculation. Jamal El Yazal, Franklyn G. Prendergast, David E. Shaw, and Yuan-Ping Pang, J. Am. Chem. Soc., 122, 11411-11415 (2000).
  29. Bis(7)-tacrine, a promising anti-Alzheimer's agent, reduces hydrogen peroxide-induced injury in rat pheochromocytoma cells: comparison with tacrine. Xiao Qiu Xiao, Nelson Tze-Kin Lee, Paul R. Carlier, Yuan-Ping Pang and Yi Fan Han, Neuroscience Letters, 290, 197-200 (2000).
  30. Protection against ischemic injury in primary cultured astrocytes of mouse cerebral cortex by bis(7)-tacrine, a novel anti-Alzheimer's agent. Yi-Fan Han, Dong-Cheng Wu, Xiao-Qiu Xiao, Priscilla M. Y. Chen, Wilson Chung, Nelson T. K. Lee, Yuan-Ping Pang and Paul R. Carlier, Neuroscience Letters, 288, 95-98 (2000).
  31. Proton Dissociation Energies of Zinc-Coordinated Hydroxamic Acids and Their Relative Affinities for Zinc: Insights into Design of Zinc Proteinase Inhibitors. Jamal El Yazal and Yuan-Ping Pang, J. Phys. Chem. B, 104, 6499-6504 (2000).
  32. Zinc's Affect on Proton Transfer between Imidazole and Acetate Predicted by ab Initio Calculations. Jamal El Yazal, Rachel R. Roe, and Yuan-Ping Pang, J. Phys. Chem. B, 104, 6662-6667 (2000).
  33. Dimerization of an Inactive Fragment of Huperzine A Produces a Drug with Twice the Potency of the Natural Product. Paul R. Carlier, Da-Ming Du, Yi-Fan Han, Jing Liu, Emanuele Perola, Ian D. Williams, and Yuan-Ping Pang, Angew. Chem. Int. Ed. Engl., 39, 1775-1777 (2000).
  34. Bis(7)-Tacrine, a Novel AChE Inhibitor, Reverses AF64A-Induced Spatial Memory Impairment in Rats. Jing Liu, Wing-Lok Ho, Nelson Tze-Kin Lee, Paul R Carlier, Yuan-Ping Pang, Yi-Fan Han, Neuroscience Letters. 282, 165-168 (2000).
  35. Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads. Emanuele Perola, Kun Xu, Thomas M. Kollmeyer, Scott H. Kaufmann, Franklyn G. Prendergast, and Yuan-Ping Pang, J. Med. Chem., 43, 401-408 (2000).
  36. Novel Zinc Protein Molecular Dynamics Simulations: Steps Toward Antiangiogenesis for Cancer Treatment. Yuan-Ping Pang, J. Mol. Model., 5, 196-202 (1999).
  37. Ab Initio Calculations of Proton Dissociation Energies of Zinc Ligands: Hypothesis of Imidazolate as Zinc Ligand in Proteins. Jamal El Yazal and Yuan-Ping Pang, J. Phys. Chem. B, 103, 8773-8779 (1999).
  38. Ab Initio Calculations of Proton Dissociation Energies of Zinc Ligands: Hypothesis of Imidazolate as Zinc Ligand in Proteins. Jamal El Yazal and Yuan-Ping Pang, J. Phys. Chem. B, 103, 8773-8779 (1999).
  39. Attenuation of scopolamine-induced deficits in navigational memory performance in rats by bis(7)-tacrine, a novel dimeric AChE inhibitor. H. Wang, P. R. Carlier, W.L. Ho, N.T.K. Lee, Y.-P. Pang, and Y.F. Han, Acta Pharmacologica Sinica 20, 211-217 (1999).
  40. Effects of bis(7)-THA, a novel promising Alzheimer's therapeutic, on rat brain acetylcholinesterase. H. Wang, P. R. Carlier, W.-L. Ho, N. T. K. Lee, C. R. L. Li, Y.-P. Pang and Y.-F. Han, Neuroreport, 10, 789-793 (1999).
  41. Bis(7)-tacrine, a novel dimeric AChE inhibitor, is a potent GABAA receptor antagonist. C.Y. Li, H. Wang, H. Xue, P. R. Carlier, K. M. Hui, Y.-P. Pang, Z. W. Li and Y.-F. Han, Neuroreport, 10, 795-800 (1999).
  42. Computational and Experimental Studies of (2,2)-Bis(indol-1-yl-methyl)acetate Suggest the Importance of the Hydrophobic Effect in Aromatic Stacking Interactions. Y.-P. Pang, J. Miller, and P. A. Kollman, J. Am. Chem. Soc., 121, 1717-1725 (1999).
  43. Atomic Levers Control Pyranose Ring Conformations. P. E. Marszalek, Y.-P. Pang, H. Li, J. El Yazal, A. F. Oberhauser, and J. M. Fernandez, Proc. Natl. Acad. Sci. USA 96, 7894-7898 (1999).
  44. Polysaccharide Elasticity Governed by Chair-Boat Transition of the Glucopyranose Ring. Piotr E. Marszalek, Andres F. Oberhauser, Yuan-Ping Pang, and Julio M. Fernandez, Nature, 396, 661-664 (1998).
  45. Highly Potent, Selective, and Low-cost bis-Tetrahydroaminacrine Inhibitors of Acetylcholinesterase: Steps Toward Novel Drugs for Treating Alzheimer's Disease. Yuan-Ping Pang, Polly Quiram, Tanya Jelacic, Feng Hong, and Stephen Brimijoin, rapid communication, J. Biol. Chem., 271, 23646-23649 (1996).
  46. Proposed Ligand Binding Site of the Transmembrane Neurotensin Receptor. Yuan-Ping Pang, Bernadette Cusack, Karen Groshan, and Elliott Richelson, J. Biol. Chem., 271, 15060-15068 (1996).
  47. Applications of Free Energy Derivatives to Analog Design. Yuan-Ping Pang and Peter A. Kollman, Perspectives in Drug Discovery and Design, 3, 106-122 (1995).
  48. Prediction of 1-Benzyl-4-[(5,6-dimethoxy-1-indanone-2-yl)methyl]piperidine's Binding Site in Acetylcholinesterase by Docking Studies with the SYSDOC Program. Yuan-Ping Pang and Alan P. Kozikowski, J. Comput.-Aided Mol. Design, 8, 682-693 (1994).
  49. Prediction of Huperzine A's Binding Sites in Acetylcholinesterase by Docking Studies. Yuan-Ping Pang and Alan Kozikowski, J. Comput.-Aided Mol. Design, 8, 669-681 (1994).
  50. Rational Design of Novel Neurotensin Mimetics: Discovery of a Pharmacologically Unprecedented Agent Exhibiting Concentration-Dependent Dual Effects as Antagonist and Full Agonist. Yuan-Ping Pang, Javid Zaidi, Alan P. Kozikowski, Bernadette Cusack, and Elliott Richelson, J. Comput.-Aided Mol. Design, 8, 433-440 (1994).
  51. A Route to Optically Pure (-)-Huperzine A; Molecular Modeling and In Vitro Pharmacology. Fumio Yamada, Alan P. Kozikowski, E. R. Reddy, Yuan-Ping Pang, Jacqueline H. Miller, and Michael McKinney, J. Am. Chem. Soc., 113, 4695-4696 (1991).
  52. Synthesis of Methoxy and Hydroxy Analogues of 1,2,3,4,4a,9a-Hexahydro-4a-fluorenamine - Rigid Phencyclidine Analogues as Probes of PCP Receptor Topography. Yuan-Ping Pang and Alan P. Kozikowski, J. Org. Chem., 56, 4499-4508 (1991).
  53. Structural Determinants of Affinity for the PCP Binding Site of the NMDA Receptor Complex: Discovery of a Rigid PCP Analogue of High Binding Affinity. Alan P. Kozikowski and Yuan-Ping Pang, Mol. Pharmacol., 37, 352-357 (1990).

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