Research Topics
| Junmei WangSummaryAffiliation: Encysive Pharmaceuticals Inc Country: USA Publications
| Collaborators
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Detail Information
Publications
Automatic atom type and bond type perception in molecular mechanical calculationsJunmei 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...- 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... - Development of reliable aqueous solubility models and their application in druglike analysisJunmei 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)... - Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SAJunmei 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... - Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretionJunmei 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... - Fast approaches for molecular polarizability calculationsJunmei 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... - Development and testing of a general amber force fieldJunmei 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... - 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 antagonistChengde 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%)... - 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.... - ADME evaluation in drug discovery. 8. The prediction of human intestinal absorption by a support vector machineTingjun 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... - ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classificationTingjun 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... - 3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approachJian-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.... - Threshold dissociation and molecular modeling of transition metal complexes of flavonoidsJunmei 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... 
Continuum polarizable force field within the Poisson-Boltzmann frameworkYu 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...- A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculationsYong 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... - Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand designShuanghong 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... 
Complete assignments of 1H and 13C NMR data for three new arylnaphthalene lignan from Justicia procumbensGuorui 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...- Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulationsCarolyn 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... - GPCR structure-based virtual screening approach for CB2 antagonist searchJian 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.... - Recent advances in computational prediction of drug absorption and permeability in drug discoveryTingjun 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... - New-generation amber united-atom force fieldLijiang 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... - Identification of a specific inhibitor of the dishevelled PDZ domainJufang 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... - Characterization of flavonoids by aluminum complexation and collisionally activated dissociationJunmei 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... - Yeast expression and NMR analysis of the extracellular domain of muscle nicotinic acetylcholine receptor alpha subunitYun 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...