Computer-Aided Drug Design | Pharmacometrics | Computational Chemistry/Biology | Chemical Informatics



PUBLICATIONS

  • Citations
1. Total citations: > 10500 times ISI Web of Knowledge
2. First author citations: > 7000 times ISI Web of Knowledge
3. Total citations: > 18000 times Google Scholar
4. H-index: 34 ISI Web of Knowledge

  • Publications (Reverse Chronological Order)
    Year 2015

  1. Wang, J.; et al. Application of MD simulations in studying the structures and dynamics of protein crystals. In Preparation.
  2. Wang, J.; et al. Study on the structural and dynamic features of protein crystals by using MD simulations with an external electric field. In Preparation.
  3. Wang, J.; et al. Molecular mechanism of Streptomycin passing through the MscL channel by MD simulations. In Preparation.
  4. Wang, J.; et al. Development of unified scaling factors for vibrational frequencies, internal energies and entropies in ab initio frequency analysis. In Preparation.
  5. Wang, J.; et al. The second generation of the general AMBER force field I: van der Waals parameterization, In Preparation.
  6. Wang, J.; Cieplak, P.; Luo, R.; Duan, Y. Development and test of BCC-based fast charge method for AMBER polarizable force fields, In Preparation.
  7. Wang, J.; et al. Prediction of residue-residue correlation of the PDZ domains through normal mode analysis. In Preparation.
  8. Tian, S.; Wang, J.; Li, Y.; Li, D.; Xu, L.; Hou, T. The application of in silico drug-likeness predictions in pharmaceutical research. Advanced Drug Delivery Reviews, Accepted.
  9. Wang, J.; Hou, T. Advances in Computationally Modeling Human Oral Bioavailability. Advanced Drug Delivery Reviews, In Press.

    Year 2014

  10. Zhang, Q.; Zhang, W.; Li, Y; Wang, J.; Zhang, J.; Hou, T. MORT: a powerful foundational library for computational biology and CADD. J. Cheminformatics, 6, Article No: 6, 2014.
  11. Wang, J.; Molecular dynamics simulations of a protein crystal. Bioenegetics, Editorial, 2014.

    Year 2013

  12. Zhang, Q.; Wang, J.; Guerrero, G.; Cecilia, J.; Garcia, J.; Li, Y.; Perez-Sanchez, H.; Hou, T. Accelerated conformational entropy calculations using graphic processing units. J. Chem. Info. Model., 53, 2057-2064, 2013.
  13. Xu, L.; Sun, H.; Li, Y.; Wang, J.; Hou, T. Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models. J. Phys. Chem. B, 117, 8408-8421, 2013.
  14. Tian, S.; Li, Y.; Li, D.; Xu, X.; Wang, J.; Zhang, Q.; Hou, T.; Modeling compound-target interaction network of traditional Chinese medicines for Type II diabetes mellitus: insight for polypharmacology and drug design. J. Chem. Info. Model., 53, 1787-1803, 2013.
  15. Tian, S.; Li, Y.; Wang, J.; Xu, X.; Xu, L.; Wang, X.; Chen, L.; Hou, T. Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines. J. Cheminformatics, 5, AN: 5, 2013.
  16. Zhang, Q.; Garcia, J.; Wang, J.; Hou, T.; Perez-Sanchez, H. A GPU based conformational entropy calculation method. IWBBIO (International Work-Conference on Bioinformatics and Biomedical Engineering) 2013.

    Year 2012

  17. Wang, J.; Cieplak, P.; Li, J.; Cai, Q.; Hsieh, M. J.; Luo, R.; Duan, Y. Development of polarizable models for molecular mechanical calculations IV: van der Waals parameterization. J. Phys. Chem. B, 116, 7088-7101, 2012.
  18. Wang, J.; Hou, T. Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations. J. Chem. Info. Model., 52, 1199-1212, 2012.
  19. Zhang, Q.; Zhang, W.; Li, Y.; Wang, J.; Zhang, L.; Hou, T.; A Rule-based algorithm for automatic bond type perception J. Cheminformatics, 4, AN: 26, 2012.
  20. Shen, M.; Tian, S.; Li, Y.; Li, Q.; Xu, X; Wang, J.; Hou, T. Drug-likeness analysis of traditional Chinese medicines: 1. Property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines. J. Cheminformatics, 4, AN: 31, 2012.
  21. Tian, S.; Wang, J.; Li, Y.; Xu, X.; Hou, T. Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches. Molecular Pharmaceuticals,9, 2875-2886, 2012.
  22. Wang, J.; Cieplak, P.; Cai, Q.; Hsieh, M. J.; Wang, J.; Duan, Y. Luo, R.; Development of polarizable models for molecular mechanical calculations III: Polarizable water models conforming to Thole polarization screening schemes. J. Phys. Chem. B, 116, 7999-8008, 2012.
  23. Wang, S.; Li, Y.; Wang, J.; Chen, L.; Zhang, L.; Yu, H.; Hou, T. ADME Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage. Molecular Pharmaceutics, 9, 996-1010, 2012.
  24. Cao, D.; Wang, J.; Zhou, R.; Li, Y.; Yu, H.; Zhang, G.; Hou, T. ADME Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB) - a comprehensive database of pharmacokinetic and toxic properties for drugs. J. Chem. Info. Model., 52, 1132-1137, 2012.
  25. Wang, J.; Challenges in binding free energy calculation using MM-PB/GBSA. Bioenergetics, 1, 2012.

    Year 2011

  26. Wang, J.; Cieplak, P.; Li, J.; Hou, T.; Luo, R.; Duan, Y. Development of polarizable models for molecular mechanical calculations I: Parameterization of atomic polarizability. J. Phys. Chem. B, 115, 3091-3099, 2011.
  27. Wang, J.; Cieplak, P.; Li, J.; Wang, J.; Cai, Q.; Hsieh, M. J.; Lei, H.; Luo, R.; Duan, Y. Development of polarizable models for molecular mechanical calculations II: Induced dipole models significantly improve accuracy of intermolecular interaction energies. J. Phys. Chem. B, 115, 3100-3111, 2011.
  28. Wang, J.*; Hou, T. Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficients. J. Comput. Chem., 32, 3505-3519, 2011.
  29. Wang, J.*; Hou, T. Application of molecular dynamics simulations in molecular property prediction I: Density and heat of vaporization. J. Chem. Theory Comput., 7, 2151-2165, 2011.
  30. Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Info. Model., 51:69-82, 2011. [cited 239 times]
  31. Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. J. Comput. Chem., 32, 866-877, 2011.
  32. Wang, J.; Hou, T. Recent Advances on aqueous solubility prediction. Combinatorial Chemistry & High Throughput Screening, 14, 328-338, 2011.
  33. Zhu, J.; Wang, J.; Yu, H.; Li, Y.; Hou, T. Recent Developments of In Silico Predictions of Oral Bioavailability Combinatorial Chemistry & High Throughput Screening, 14, 362-374, 2011.
  34. Tian, S.; Li Y.; Wang, J.; Zhang, J.; Hou, T. ADME evaluation in drug discovery. 9. Prediction of oral bioavailability in human based on molecular properties and structural fingerprints. Molecular Pharmaceutics, 8, 841-851, 2011.

    Year 2010

  35. Wang, J.*; Hou, T. Drug and drug candidate building block analysis. J. Chem. Info. Model., 50, 55-67, 2010.

    Year 2009

  36. Wang, J.*; Hou, T.; Xu, X. Aqueous solubility prediction based on weighted atom type counts and solvent accessible surface areas. J. Chem. Info. Model., 49, 571-581, 2009.
  37. Pierce, S.; Wang, J.; Jayawickramarajah, J.; Hamilton, A.; Brodbelt, J. Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats. Chemistry, A European Journal,15, 11244-11255, 2009 .
  38. Cieplak, P.; Dupradeau, F. Y.; Duan, Y.; Wang, J. Polarization effects in molecular mechanical force fields. J. Physics-Condensed Matter, 21, 333102, 2009.
  39. Hou, T.; Li, Y.; Zhang, W.; Wang, J. Recent developments of in silico predictions of intestinal absorption and oral bioavailability. Combinatorial Chemistry & High. Throughput Screening, 12, 497-506, 2009.

    Year 2008

  40. Hou, T.; Wang, J. Structure-ADME relationship: still a long way to go? Expert Opinion on Drug Metabolism & Toxicology, 4, 759-770, 2008.

    Year 2007

  41. Wang, J.*; Krudy, G.; Hou, T.; Holland, G.; Xu, X. Development of reliable aqueous solubility models and their application in drug-like analysis. J. Chemical Information and Modeling, 47, 1395-1404, 2007.
  42. Wang, J.; Xie, X.-Q.; Hou, T. J.; Xu, X. J. Fast approaches for molecular polarizability calculations. J. Physical Chemistry A. 111, 4443-4448, 2007.
  43. Mazzitelli, C.; Wang, J.; Brodbelt, J. Gas-Phase Stability of G-quadruplex DNA Determined by Electrospray Ionization Tandem Mass Spectrometry and Molecular Dynamics Simulations, J. Am. Soc. Mass Spectrom. 18, 1760-1773, 2007.
  44. Hou, T.; Wang, J. ADME evaluation in drug discovery 8. The prediction of intestinal absorption by support vector machine. J. Chem. Info. Model., 47, 2408-2415, 2007.
  45. Hou, T.; Wang, J.; Zhang, W.; Xu, X. ADME evaluation in drug discovery. 7. Prediction of oral absorption by correlation and classification. J. Chemical Information and Modeling, 47, 208-218, 2007.
  46. Hou, T.; Wang, J.; Zhang, W.; Xu, X. ADME evaluation in drug discovery. 6. If the oral bioavailability in human can be effectively predicted by simple molecular properties-based rules? J. Chemical Information and Modeling, 47, 460-463, 2007.
  47. Chen, J.; Wang, J.; and Xie, X.-Q., GPCR structure-based virtual screening approach for CB2 antagonist search, J. Chemical Information and Modeling, 47, 1626-1637, 2007.

    Year 2006

  48. Wang, J.*; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations, J. Mol. Grap. Mod., 25, 247-260, 2006. [cited 751 times]
  49. Wang, J.*; Krudy, G.; Xie, X.-Q.; Wu, C.; Holland, G. Genetic algorithm-optimized QSPR models for bioavailability, protein binding, and urinary excretion, J. Chem. Info. Model., 46, 2674-2683, 2006.
  50. Wang, J.*; Hou, T.; Xu, X. Recent advances in free energy calculations with a combination of molecular mechanics and continuum models, Current Computer-Aided Drug Design, 2, 95-103, 2006.
  51. Chen, J.; Han, X.; Liu, Q.; Makriyannis, A.; Wang, J.; Xie, X.-Q., 3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtype CB1 and CB2. A combined NMR and CoMFA approach, J. Med. Chem., 49, 625-636, 2006.
  52. Hou, T.; Wang, J.; Xu, X. Recent advances in computational prediction of drug absorption and permeability in drug discovery, Current Medicinal Chemistry, 13, 2653-2667, 2006.
  53. Yang, L. J.; Tan, C. H.; Hsieh, M. J.; Wang, J.; Duan, Y.; Cieplak, P.; Caldwell, J.; Kollman, P. A.; Luo, R. New-generation amber united-atom force field, J. Phys. Chem B, 110, 13166-13176, 2006.

    Year 2005

  54. Wang, J.*; Kang, X.; Kollman, P. A.; Kuntz, I. D. Hieratical database screening for HIV-1 reverse transcriptase using pharmacophore model, rigid docking, solvation docking and MM-PB/SA, J. Med. Chem. . 48, 2432-2444, 2005.
  55. Shan, J.; Shi, D.; Wang, J.; Zheng, J. Identification of a specific inhibitor of the disheveled PDZ domain, Biochemistry, 44, 15495-15503, 2005.
  56. Shan, J.; Wang, J.; Zheng, J. Identification of non-peptide inhibitor of the disheveled PDZ domain, Biophysical J., 88, 334A-334A, 2005.
  57. Zhang, J.; Brodbelt, J. S.; Wang, J. Threshold Dissociation of Transition Metal Complexes of Flavonoids. J. Am. Soc. Mass Spectrom. 16, 139-151, 2005.
  58. Zhang, J.; Wang, J.; Brodbelt, J. S. Characterization of flavonoids by aluminum complexation and collisionally activated dissociation. J. Mass Spectrom. 40, 350-363, 2005.

    Year 2004

  59. Wu,, C.; Decker, E. R.; Blok, N.; Bui, H.; You, T.; Wang, J.; Bourgoyne, A. R.; Knowles, V.; Berens, K. L.; Holland, G. W.; Brock, T. A.; Dixon, R. A. F. Discovery, modeling, and human pharmacokinetics of N-(2-acetyl-4,6-dimethylphenyl)-3-(3,4-diethylisoxazol-5-ylsulfamoyl) thiophene-2-carboxamide (TBC3711), a second generation, ETA selective, and orally bioavailable endothelin antagonist, J. Med. Chem. 47, 1969-1986, 2004.
  60. Wang, J.; Wolf, R.; Caldwell, J.; Kollman, P. A.; Case, D. A. Development and test of a general AMBER force field for organic molecules and bio-molecules, J. Comput. Chem. 25, 1157-1174, 2004. [cited 2854 times]

    Year 2003

  61. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G. M.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem. 24, 1999-2012, 2003. [cited 1849 times]

    Year 2002

  62. Huo, S.; Wang, J.; Cieplak, P.; Kollman, P. A.; Kuntz, I. D. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design, J. Med. Chem., 45, 1412-1419, 2002. [cited 134 times]

    Year 2001

  63. Wang, J.;, Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA, J. Am. Chem. Soc., 123, 5221-5230, 2001. [cited 387 times]
  64. Wang, J.;, Wang, W.; Huo, S.; Lee M.; Kollman, P. A. A solvation model based on weighted solvent accessible surface area, J. Phys. Chem. B., 105, 5055-5067, 2001.
  65. Wang, J.; Kollman, P. A., Automatic parameterization of force field by systematic search and genetic algorithms, J. Comput. Chem., 22, 1219-1228, 2001.
  66. Wang, W.; Lim, W.; Jakalian, A.; Wang, J.; Luo, R.; Bayly, C.; Kollman, P. A. An analysis of the interaction between the sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations and sequence analysis, J. Am. Chem. Soc., 123, 3986-3994, 2001.

    Year 2000

  67. Wang, J.;, Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) mode perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074, 2000. [cited 2187 times]

    Before Year 2000

  68. Xu, X.; Hou, T.; Wang, J.; Liao, N.; Lo, H.; Guo, S. New molecular design system-PUMDS based on intermolecular interactions, Jisuanji Yu Yingyong Huaxue, 16, 335-336, 1999.
  69. Gao H.; Wang, J. Calculation of chemical stability of 4 typical derivatives of lipoic acid, Zhongguo Yaowu Huaxue Zazhi, 9, 50-52, 1999.
  70. Wang, J.; Zhang, H.; Xu, X. Theoretical studies on force titration of amino group-terminated self-assembled monolayers, J. Mol. Struct. (THEM), 451, 295-303, 1998.
  71. Hou, T.; Wang, J.; Li, Y.; Xu, X. Application of genetic algorithm to the QSAR research of pyrrolobenzothiazepinones and pyrrolobenzoxazepinones-novel and specific non-nucleoside HIV-1 reverse transcription inhibitors, Chinese Chemical Letters, 9, 651-654, 1998.
  72. Wang, J.; Hou, T.; Li, Y.; Xu, X. The QSAR research of pyrrolobenzothiazepinones and pyrrolobenzoxazepinones – novel and specific non-nucleoside HIV-1 reverse transcriptase inhibitors, Chinese Chemical Letters, 8, 889-892, 1997.
  73. Wang, J.; Xu, X.; Jian, F. A modified soft docking method for proteins and peptides, Chinese Chemical Letters, 8, 615-618, 1997.
  74. Wang, J.; Zhao, Z.; Ye, X. QSAR studies of morphinones and its analogous, J. Graduate School, Academic Sinica, 14, 35, 1997.
  75. He, H.; Wang, J.; Xu, X.; Liu, Z. Force titration of self-assembled monolayer using chemical force microscopy, Acta Physico-Chimica Sinca, 13, 293-296, 1997.
  76. Wang, J.; Ye, X. Conformational analysis and quantum mechanical studies of morphiceptine, Acta Pharmaceutical Sinica, 31, 502-508, 1996.
  77. Wang, J.; Zhao, Z.; Ye, X. Parameterization procedures in molecular mechanical calculations, Acta Physico-Chimica Sinica, 11, 424-428, 1996.
  78. Zhao, B.; Lu, X.; Wang, J.; Ye, X.; Lu, C. Study of spatial characters of N-(acetylglycyl)methionine sulfoximine methyl ester, Beijing Huagong Daxue Xuebao, Ziran Kexueban, 23, 76-79, 1996.
  79. Wang, J.; Hu, Z.; Ye, X. Conformational analysis of Leu-enkephalin by molecular dynamics simulations, Acta Physico-Chimica Sinica, 11, 673-677, 1995.
  80. Wang, J.;, Hou, T.; Chen, L.; Xu, X. Conformational analysis of peptides using Monte Carlo simulations combined with the genetic algorithm, Chemometrics and intelligent laboratory systems, 45, 347-351, 1999.
  81. Wang, J.; Hou, T.; Chen, L.; Xu, X. Automated docking of peptides and proteins by genetic algorithm, Chemometrics and intelligent laboratory systems, 45, 281-286, 1999.
  82. Hou, T.; Wang, J.; Chen, L.; Xu, X.; Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search, Protein Engineering, 12, 639-647, 1999.
  83. Hou, T.; Wang, J.; Xu, X. Application of genetic algorithm on the structure activity correlation study of a group of non-nucleoside HIV-1 RT inhibitors, Chemometrics and intelligent laboratory systems, 45, 303-310, 1999.
  84. Hou, T.; Wang, J.; Liao N.; Xu, X.; Application of genetic algorithm on the structure activity relationship analysis of some cinnamamides, J. Chem. Info. Comput. Sci., 39, 775-781, 1999.
  85. Hou, T.; Wang, J.; Xu, X. A comparison of three heuristic algorithms for molecular docking, Chinese Chemical Letters, 10, 615-618, 1999.
  86. Xie, G.; Kong, Y.; Wang, J.; Xu, X.; Jin, S. Studies on crystal structure, conformation analysis and electronic property of a new designed hapten containing sulfur, Gaodeng Xuexiao Huaxue Xuebao, 20, 890-894, 1999.

    Book Chapters

  87. Case, D. A.; Darden, T.; Cheatham III, T. E.; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; et al. AMBER 12, University of California, San Francisco, 2012. [Google Scholar: cited 133 times]
  88. Wang, J.; Hou, T.; Recent Advances on in silico ADME Modeling. Annual Report Computational Chemistry, Chapter 5, 2010.
  89. Case, D. A.; Darden, T.; Cheatham III, T. E.; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; et al. AMBER 11, University of California, San Francisco, 2010. [Google Scholar: cited 554 times]
  90. Case, D. A.; Darden, T.; Cheatham III, T. E.; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; et al. AMBER 10, University of California, San Francisco, 2008. [Google Scholar: cited 801 times]
  91. Case, D. A.; Darden, T.; Cheatham III, T. E.; Simmerling, C.; Wang, J.; Duke, R. E.; Luo, R.; et al. AMBER 9, University of California, San Francisco, 2006. [Google Scholar: cited 1413 times]
  92. Case, D. A.; Darden, T.; Cheatham III, T. E.; Simmerling, C. L.; Wang, J.; Merz, K. M.; et al. AMBER 8, University of California, San Francisco, 2004. [Google Scholar: cited 1110 times]
  93. Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham III, T. E.; Wang, J.; Ross, W. S.; et al. AMBER 7, University of California, San Francisco, 2002. [Google Scholar: cited 515 times]
  94. Kuhn, B.; Donini, O.; Huo, S.; Wang, J.; Kollman, P. A. MM-PBSA applied to computer-assisted ligand design, Free Energy Calculations in Rational Drug Design, 243-251. Editor(s): Reddy, M.; Rami, E.; Mark, D. Publisher: Kluwer Academic/Plenum Publishers, New York, N. Y., 2001.