Junmei Wang

Summary

Affiliation: Encysive Pharmaceuticals Inc
Country: USA

Publications

  1. ncbi Automatic atom type and bond type perception in molecular mechanical calculations
    Junmei Wang
    College of Chemistry, Peking University, Beijing 100871, China
    J Mol Graph Model 25:247-60. 2006
  2. ncbi Structure-ADME relationship: still a long way to go?
    Tingjun Hou
    University of California at San Diego, Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, 9500 Gilman Drive, La Jolla, CA 92093 0359, USA
    Expert Opin Drug Metab Toxicol 4:759-70. 2008
  3. ncbi Development of reliable aqueous solubility models and their application in druglike analysis
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, Texas 77030, USA
    J Chem Inf Model 47:1395-404. 2007
  4. ncbi Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Med Chem 48:2432-44. 2005
  5. ncbi Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, Texas 77030, USA
    J Chem Inf Model 46:2674-83. 2006
  6. ncbi Fast approaches for molecular polarizability calculations
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, TX 77030, USA
    J Phys Chem A 111:4443-8. 2007
  7. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
  8. ncbi Discovery, modeling, and human pharmacokinetics of N-(2-acetyl-4,6-dimethylphenyl)-3-(3,4-dimethylisoxazol-5-ylsulfamoyl)thiophene-2-carboxamide (TBC3711), a second generation, ETA selective, and orally bioavailable endothelin antagonist
    Chengde Wu
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, TX 77030, USA
    J Med Chem 47:1969-86. 2004
  9. ncbi ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules?
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Chem Inf Model 47:460-3. 2007
  10. ncbi ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Chem Inf Model 47:2408-15. 2007

Collaborators

Detail Information

Publications24

  1. ncbi Automatic atom type and bond type perception in molecular mechanical calculations
    Junmei Wang
    College of Chemistry, Peking University, Beijing 100871, China
    J Mol Graph Model 25:247-60. 2006
    ..for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types...
  2. ncbi Structure-ADME relationship: still a long way to go?
    Tingjun Hou
    University of California at San Diego, Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, 9500 Gilman Drive, La Jolla, CA 92093 0359, USA
    Expert Opin Drug Metab Toxicol 4:759-70. 2008
    ..Theoretical models for predicting absorption, distribution, metabolism and excretion (ADME) properties play increasingly important roles in support of the drug development process...
  3. ncbi Development of reliable aqueous solubility models and their application in druglike analysis
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, Texas 77030, USA
    J Chem Inf Model 47:1395-404. 2007
    ..We concluded that the two models could be served as a rule in druglike analysis and an efficient filter in prioritizing compound libraries prior to high throughput screenings (HTS)...
  4. ncbi Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Med Chem 48:2432-44. 2005
    ..8 kcal/mol and the best one, HIT15, had -17.0 kcal/mol. In conclusion, the hierarchical multiple-filter database searching strategy is an attractive strategy in drug lead exploration...
  5. ncbi Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, Texas 77030, USA
    J Chem Inf Model 46:2674-83. 2006
    ..On the other hand, the opposite trend was observed for ACD (Available Chemicals Directory), a database of all kinds of available compounds...
  6. ncbi Fast approaches for molecular polarizability calculations
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin Street, Houston, TX 77030, USA
    J Phys Chem A 111:4443-8. 2007
    ..It is expected that both model 1A and model 2E will have broad applications in QSAR and QSPR studies...
  7. ncbi Development and testing of a general amber force field
    Junmei Wang
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, Texas 77030, USA
    J Comput Chem 25:1157-74. 2004
    ..The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching...
  8. ncbi Discovery, modeling, and human pharmacokinetics of N-(2-acetyl-4,6-dimethylphenyl)-3-(3,4-dimethylisoxazol-5-ylsulfamoyl)thiophene-2-carboxamide (TBC3711), a second generation, ETA selective, and orally bioavailable endothelin antagonist
    Chengde Wu
    Encysive Pharmaceuticals Inc, 7000 Fannin, Houston, TX 77030, USA
    J Med Chem 47:1969-86. 2004
    ..08 nM), and optimal ET(A)/ET(B) selectivity (441 000-fold). Compound 7z has completed phase-I clinical development and was well tolerated with desirable pharmacokinetics in humans (t(1/2) = 6-7 h, oral availability > 80%)...
  9. ncbi ADME evaluation in drug discovery. 6. Can oral bioavailability in humans be effectively predicted by simple molecular property-based rules?
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Chem Inf Model 47:460-3. 2007
    ....
  10. ncbi ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machine
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    J Chem Inf Model 47:2408-15. 2007
    ..Our work illustrates that SVMs used in combination with simple molecular descriptors can provide an extremely reliable assessment of intestinal absorption in an early in silico filtering process...
  11. ncbi ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093, USA
    J Chem Inf Model 47:208-18. 2007
    ..The databases of human intestinal absorption reported here are available for download from the supporting Web site: http://modem.ucsd.edu/adme...
  12. ncbi 3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approach
    Jian Zhong Chen
    Department of Pharmaceutical and Pharmacological Sciences, College of Pharmacy, University of Houston, Texas 77204 5037, USA
    J Med Chem 49:625-36. 2006
    ....
  13. ncbi Threshold dissociation and molecular modeling of transition metal complexes of flavonoids
    Junmei Zhang
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 16:139-51. 2005
    ..The conformations were combined with the point charges and helium accessible surface areas to explain qualitatively the differences in threshold energies for isomeric flavonoids...
  14. pmc Continuum polarizable force field within the Poisson-Boltzmann framework
    Yu Hong Tan
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697 3900, USA
    J Phys Chem B 112:7675-88. 2008
    ..Given the development documented here, the next natural step is the construction of a full protein/nucleic acid force field within the new continuum polarization framework...
  15. ncbi A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    Yong Duan
    Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
    J Comput Chem 24:1999-2012. 2003
    ..charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed...
  16. ncbi Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design
    Shuanghong Huo
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, California 94143 0446, USA
    J Med Chem 45:1412-9. 2002
    ..This study offers hope that current methods of estimating the free energy of binding are accurate enough to be used in a multistep virtual screening protocol...
  17. doi Complete assignments of 1H and 13C NMR data for three new arylnaphthalene lignan from Justicia procumbens
    Guorui Liu
    Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, P R China
    Magn Reson Chem 46:283-6. 2008
    ..The complete assignments of 1H and 13C NMR data for three new lignans were first obtained by means of 2D NMR techniques, including HSQC and HMBC...
  18. pmc Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 18:1760-73. 2007
    ..This discrepancy is attributed to differences in the fragmentation pathway of the quadruplex...
  19. ncbi GPCR structure-based virtual screening approach for CB2 antagonist search
    Jian Zhong Chen
    Department of Pharmaceutical Sciences, School of Pharmacy, Pittsburgh Molecular Library Screening Center, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    J Chem Inf Model 47:1626-37. 2007
    ....
  20. ncbi Recent advances in computational prediction of drug absorption and permeability in drug discovery
    Tingjun Hou
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093, USA
    Curr Med Chem 13:2653-67. 2006
    ..Recent developments in the prediction of drug absorption, especially with the application of new machine learning methods and newly developed software are also discussed. Future directions for research are outlined...
  21. ncbi New-generation amber united-atom force field
    Lijiang Yang
    Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
    J Phys Chem B 110:13166-76. 2006
    ..The new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide...
  22. ncbi Identification of a specific inhibitor of the dishevelled PDZ domain
    Jufang Shan
    Department of Structural Biology, St Jude Children s Research Hospital, Memphis, Tennessee 38105, USA
    Biochemistry 44:15495-503. 2005
    ..This compound provides a basis for rational design of high-affinity inhibitors of the PDZ domain, which can block Wnt signaling by interrupting the Fz-Dvl interaction...
  23. ncbi Characterization of flavonoids by aluminum complexation and collisionally activated dissociation
    Junmei Zhang
    Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
    J Mass Spectrom 40:350-63. 2005
    ..The conformations of the complexes, which involve multiple interactions between the aglycone and disaccharide portions of the flavonoid with the metal ion, are significantly different for the isomeric flavonoids...
  24. ncbi Yeast expression and NMR analysis of the extracellular domain of muscle nicotinic acetylcholine receptor alpha subunit
    Yun Yao
    Department of Neurobiology, University of Pittsburgh School of Medicine, 3500 Terrace Street, Pittsburgh, PA 15261, USA
    J Biol Chem 277:12613-21. 2002
    ..We conclude that the soluble AChR protein is useful for high resolution structural studies...