2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 Book

2020

  • Jing, Y.; Hu, Z.; Fan, P.; Xue, Y.; Wang, L.; Tarter, R.; Kirisci, L.; Wang, J.; Vanyukov, M.; Xie, X.-Q. Analysis of substance use and its outcomes by machine learning I. Childhood evaluation of liability to substance use disorder. Drug & Alcohol Dependence, 206, Article Number: 107605, 2020 (DOI: 10.1016/j.drugalcdep.2019.107605)

  • Hu, Z.; Jing, Y.; Xue, Y.; Fan, P.; Wang, L.; Vanyukov, M.; Kirisci, L.; Wang, J.; Tarter, R.; Xie, X.-Q.* Analysis of substance use and its outcomes by machine learning: II. Derivation and prediction of the trajectory of substance use severity. Drug & Alcohol Dependence, 206, Article Number: 107604, 2020 (DOI: 10.1016/j.drugalcdep.2019.107604)

  • Xing, C.; Zhuang, Y.; Xu, T.-H.; Feng, Z.; Zhou, X.; Chen, M.; Wang, L.; Meng, X.; Xue, Y.; Wang, J.; Liu, H.; McGuire, T.; Zhao, G.; Melcher, K.; Zhang, C.; Xu, E.; Xie, X.-Q. Cryo-EM Structure of the Human Cannabinoid Receptor CB2-G(i) Signaling Complex. Cell, 180 (4), 645-654.e13, 2020. (DOI: 10.1016/j.cell.2020.01.007)

  • Zhai, J.; Liu, S.; Ji, B.; Zhang, Y.; Wang, J. PBPK Models of Two CNS Stimulants, Amphetamine and Methylphenidate, for Clinical Dosing Regimen Optimizations. Archives of Pharmaceuticals & Pharmacology Research. Article Number: 000545, 2020 (DOI: 10.33552/APPR.2019.02.000545)

  • Wang J. Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study. Chemrxiv, 2020. Link

  • He, X.; Liu, S.; Lee. T.-S.; Ji, B.; Man, V.; York, D.; Wang, J. Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF. ACS Omega, 5, 9, 4611-4619, 2020. Link

  • Ji, B.; Liu, S.; He, X.; Man, V.; Xie, X.-Q.; Wang, J. Prediction of the binding affinities and selectivity for CB1 and CB2 ligands using homology modeling, molecular docking, molecular dynamics simulations, and MM-PBSA binding free energy calculations. ACS Chemical Neuroscience, 11, 8, 1139-1158, 2020.

  • Bogetti, X.; Ghosh, S.; Gamble, J. A.; Wang, J.; Saxena, S. Molecular Dynamics simulations based on newly developed force field parameters for Cu(II) spin labels provide insights into Double Histidine-based Double Electron-Electron Resonance. Journal of Physical Chemistry B. 124, 14, 2788-2797, 2020.

  • Wray, R.; Wang, J.; Iscla, I.; Blount, P. Novel MscL agonists that allow multiple antibiotics cytoplasmic access activate the channel through a common binding site. PLOS One, 0228153, 2020. Link

  • Hu, Z.; Jing, Y.; Xue, Y.; Fan, P.; Wang, L.; Vanyukov, M.; Kirisci, L.; Wang, J.; Tarter, R.; Xie, X.-Q. Analysis of substance use and its outcomes by machine learning: II. Derivation and prediction of the trajectory of substance use severity. Drug & Alcohol Dependence, 206, Article Number: 107604, 2020 (DOI: 10.1016/j.drugalcdep.2019.107604)

  • Man, V.; He, X.; Ji, B.; Liu, S.; Xie, X.-Q.; Wang, J. Introducing Virtual Oligomerization Inhibition to Identify Potent Inhibitors of Aβ Oligomerization. J. Chem. Theory & Computation, In Press.

  • Wang J. Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study. J. Chem. Info. Model., In Press.

  • Wang, E.; Liu, H.; Wang, J.; Weng, G.; Sun, H.; Wang, Z.; Kang, Y.; Hou, T. Development and Evaluation of MM/GBSA based on a Variable Dielectric GB Model for Predicting Protein-Ligand Binding Affinities, J. Chem. Info. Model., In Press. (DOI: 10.1021/acs.jcim.0c00024)

  • Xue, Y.; Hu, Z. (co-first author); Wu, H.; Li X.; Wang, J.; Lv QZ; Xie, XQ. Efficacy Assessment of Ticagrelor versus Clopidogrel in Chinese Patients with Acute Coronary Syndrome Undergoing Percutaneous Coronary Intervention by Data Mining and Machine-Learning Decision Tree Approaches. J. Clinical Pharmacy and Therapeutics, Accepted.

  • Kim, P.; Li, H.; Wang, J.; Zhao, Z. Landscape of drug-resistance mutations in kinase regulatory hotspots (Manuscript ID: BIB-20-0148). Briefings in Bioinformatics, Accepted.

  • Derreumaux, P.; Man, V.; Wang, J.; Nguyen, P. Tau R3-R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations. J. Phys. Chem. B. Accepted.

2019

  • Wray, R.; Iscla, I.; Kovacs, Z.; Wang, J.; Blount, P. Novel compounds that specifically bind and modulate MscL: insights into channel gating mechanisms, FASEB Journal, 33, 3180-3189, 2019.

  • Taylor, C.; Cormier, K.; Keenan, S.; Earnest, S.; Stippec, S.; Wichaidit C.; Juang, Y.; Wang, J.; Shvartsman, S.; Goldsmith, E.; Cobb, M. Functional divergence caused by mutations in an energetic hotspot in ERK2. PNAS, 116 (31), 15514-15523, 2019.

  • Wang, J.; Ge, Y.; Xie, X.-Q. Development and testing of druglike screening libraries. J. Chem. Inf. Model., 59, 53-65, 2019.

  • Man, V.; He, X.; Derreumaux, P.; Ji, B.; Xie, X.-Q.; Nguyen, P.; Wang, J. Effects of all-atom molecular mechanics force fields on Amyloid peptide assembly: the case of Aβ16-22 Dimer. J. Chem. Theor. Comput. 15, 1440-1452, 2019.

  • Wang, J.; Cieplak, P.; Luo, R.; Duan, Y. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization to Reproduce Ab Initio Anisotropy. J. Chem. Theor. Comput. 15, 1146-1158, 2019.

  • Man, V.; Truong, P.; Li, M.; Wang, J.; Van-Oanh, N.-T.; Derreumaux, P.; Nguyen, P. Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation, J. Phys. Chem. B, 123, 71-78, 2019.

  • Bian, Y.; He, X.; Jing, Y.; Wang, L.; Wang, J.; Xie, X.-Q. “Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation”, Acta Pharmacologica Sinica, 40, 374-386, 2019.

  • Wu, N.; Feng, Z.; He, X.; Kwon, T.; Wang, J.; Xie, X.-Q. Insight of Captagon Abuse by Chemogenomics Knowledgebase-guided System Pharmacology Target Mapping Analyses. Scientific Reports, 9:2268, 2019.

  • Yin, J.; Chapman, K.; Clark, L. D.; Shao, Z.; Borek, D.; Xu, Q.; Wang, J.; Rosenbaum, D.; Crystal structure of the human NK1 tachykinin receptor. PNAS, 115, 13264-13269, 2019.

  • Ge, H.; Bian, Y.; He, X.; Qian, K.; Xie, X.-Q.; Wang, J. L- Tetrahydroberberrubine shows antagonistic effects on Dopamine D1 and D2 receptors. J. Comput.-Aided Mol. Des., 33, 447-459, 2019.

  • Su, L.; Wang, Y.; Wang, J.; Moresco, E.; Boger, D.; Beutler, B. Zhang, H. Structural basis of TLR1/TLR2 activation by a synthetic agonist Diprovocim. J. Med. Chem, 62, 2938-2949, 2019.

  • Man, V.; Li, M.; Wang, J.; Derreumaux, P. and Nguyen, P. Nonequilibrium Atomistic Molecular Dynamics Simulation of Tubular Nano-motor Propelled by Bubble Propulsion. J. Chemical Physics, 150 (21), 024103, 2019.

  • Man, V.; Li, M.; Wang, J.; Derreumaux, P. and Nguyen, P. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level. J. Chemical Physics, 150 (21), 215101, 2019.

  • Wang, E.; Sun, H.; Wang, J.; Wang, Z.; Liu Hui, Zhang, J.; Hou, T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chemical Reviews, 119(16), 9478-9508, 2019.

  • Ji, B.; Liu, S.; Xue, Y.; He, X.; Man, V.; Xie, X.-Q., Wang, J. Prediction of Drug-Drug Interactions Between Opioids and Overdose Benzodiazepines Using Physiologically-Based Pharmacokinetic (PBPK) Modeling and Simulation, Drugs in R&D, 19 (3), 297-305, 2019.

  • Man, V.; He, X.; Ji, B.; Liu, S.; Xie, X.-Q., Wang, J. The Dependence of Amyloid-β42 Self-Assembly on The Monomer Concentrations, ACS Chemical Neuroscience, 10 (11), 4643-4658, 2019.

  • Wray, R.; Herrera, N.; Iscla, I.; Wang, J.; Blount, P. An agonist of the MscL channel affects multiple bacterial species and increases membrane permeability and potency of common antibiotics. Mol MicroBiol. 112 (3), 896-905, 2019.

  • Bian, Y., Wang, J. Xie XQ., Deep convolutional generative adversarial network (dcGAN) models for the de novo design of small molecules targeting cannabinoid receptors. Molecular Pharmaceuticals, 16 (11), 4451-4460, 2019.

  • Liu, S.; Ji, B.; He, X.; Man, V.; Liu, J. Wang, J. New Application of In Silico Methods in Identifying Key Components of the Anti-Cancer Herbal Formulation YIV-906 (PHY906), Physical Chemistry and Chemical Physics., 21 (42), 23501-23513, 2019.

  • Taylor, C.; Cormier, K.; Keenan, S.; Earnest, S.; Stippec, S.; Wichaidit C.; Juang, Y.; Wang, J.; Shvartsman, S.; Goldsmith, E.; Cobb, M. Functional divergence caused by mutations in an energetic hotspot in ERK2. PNAS, 116 (31), 15514-15523, 2019.

2018

  • Dominik, D.; Man, V.; Van-Oanh, N.-T.; Wang, J.; Kawasaki, T.; Derreumaux, P.; Nguyen, P. Breaking down cellulose fibrils with a mid-infrared laser, Cellulose, 25, 5553-5568, 2018.

  • Suno, R.; Kimura, K.; Nakane, T.; Yamashita, K.; Wang, J.; Fujiwara, T.;, Yamanaka, Y.; Im, D.; Horita, S.; Tsujimoto, H.; Tawaramoto, M.; Hirokawa, T.; Nango, E.; Tono, K.; Kameshima, T.; Hatsui, T.; Joti, Y.; Yabashi, M.; Shimamoto, K.; Yamamoto, M.; Rosenbaum, D. Iwata, S.; Shimamura, T.; Kobayashi, T. Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. Structure, 26, 7-19, 2018.

  • Shang, J.; Hu, B.; Wang, J.; Zhu, F.; Kang, Y.; Li, D.; Sun, H.; Long, D.-X.; Hou, T. A cheminformatic insight into the differences between terrestrial and marine originated natural products, J. Chem. Info. Mod. 58, 1182-1193, 2018.

  • Xavier, B.; Zein, A.; Wang J.; Lee, J.-Y. Structural snapshot of the cholesterol-transport ABC proteins, Biochemistry & Cell Biology, 97, 224-233, 2018.

  • Chen, F.; Sun, H.; Wang, J.; Liu, H.; Wang, Z.; Lei, T.; Li, Y. Hou, T. Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes, 24, 1183-1194, 2018.

  • Wang, Y.; Lin, W.; Wu, N.; Wang, J.; Feng, Z.; Xie, X.-Q. An Insight of Acetaminophen and its Metabolites using Molecular Docking and Molecular Dynamics Simulation, J. Mol. Modeling, 24:243, 2018.

  • Liu, N.; Zhou, W.; Guo, Y.; Wang, J.; Fu, W.; Sun, H.; Li, D.; Duan, M.; Hou, T. Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and its Coactivator. J. Chem. Info. Model., 58, 1652-1661, 2018.

  • He, X.; Man, V.; Ji, B.; Xie, X.-Q.; Wang, J. Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. J. Comput.-Aided Mol. Des. 33, 105-117, 2018.

2017

  • Li, X.; Diao, J.; Greene, D.; Wang, J.; Luo, R. A continuum Poisson-Boltzmann model for membrane channel proteins”, J. Chem. Teor. Comput., 13, 3398-3412, 2017.

2016

  • Wray, R.; Iscla, I.; Wang, J.; Blount P. Dihydrostreptomycin directly binds to, modulates, and passes through the MscL channel pore. PLOS Biology, 14, e1002473, 2016.
  • Shao, Z. H.; Yin, J.; Chapman, K.; Grzemska, M.; Clark, L.; Wang, J.; Rosenbaum, D. "High-resolution crystal structure of the human CB1 cannabinoid receptor", Nature, 540, 602-606, 2016.
  • Lee, J.-Y. ; Kinch, L. N.; Borek, D. M.; , Wang, J.; Wang, J.; Urbatsch, I. L.; Xie, X.-S.; Grishin, N. V.; Cohen, J. C.; Otwinowski, Z.; Hobbs, H. H.; Rosenbaum, D. M., Crystal structure of the human sterol transporter ABCG5/ABCG8, Nature, 533, 561-564, 2016.

2015

  • Wang, J.; Hou, T. Advances in Computationally Modeling Human Oral Bioavailability. Advanced Drug Delivery Reviews, 86, 11-16, 2015.
  • 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, 86, 2-10, 2015.

2014

  • 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.
  • Wang, J.; Molecular dynamics simulations of a protein crystal. Bioenegetics, Editorial, 2014.

2013

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2012

  • 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.
  • 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, 201
  • Wang, J.; Challenges in binding free energy calculation using MM-PB/GBSA. Bioenergetics, 1, 2012.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2011

  • 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.
  • 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.
  • Wang, J.*; Hou, T. Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficients. J. Comput. Chem., 32, 3505-3519, 2011.
  • 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.
  • 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.
  • 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.
  • Wang, J.; Hou, T. Recent Advances on aqueous solubility prediction. Combinatorial Chemistry & High Throughput Screening, 14, 328-338, 2011.
  • 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.
  • 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.

2010

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

2009

  • 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.

  • 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.

  • Cieplak, P.; Dupradeau, F. Y.; Duan, Y.; Wang, J. Polarization effects in molecular mechanical force fields. J. Physics-Condensed Matter, 21, 333102, 2009.

  • 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.

2008

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

2007

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2006

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

2005

  • 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.

  • Shan, J.; Shi, D.; Wang, J.; Zheng, J. Identification of a specific inhibitor of the disheveled PDZ domain, Biochemistry, 44, 15495-15503, 2005.

  • Shan, J.; Wang, J.; Zheng, J. Identification of non-peptide inhibitor of the disheveled PDZ domain, Biophysical J., 88, 334A-334A, 2005.

  • Zhang, J.; Brodbelt, J. S.; Wang, J. Threshold Dissociation of Transition Metal Complexes of Flavonoids. J. Am. Soc. Mass Spectrom. 16, 139-151, 2005.

  • Zhang, J.; Wang, J.; Brodbelt, J. S. Characterization of flavonoids by aluminum complexation and collisionally activated dissociation. J. Mass Spectrom. 40, 350-363, 2005.

2004

  • 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.
  • 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.

2003

  • 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.

2002

  • 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.

2001

  • 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.
  • 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.
  • Wang, J.; Kollman, P. A., Automatic parameterization of force field by systematic search and genetic algorithms, J. Comput. Chem., 22, 1219-1228, 2001.
  • 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.

2000

  • 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.

Book

  • 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]
  • Wang, J.; Hou, T.; Recent Advances on in silico ADME Modeling. Annual Report Computational Chemistry, Chapter 5, 2010.
  • 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]
  • 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]
  • 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]
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