Youyong Li

Professor

Institute of Functional Nano and Soft Materials

Soochow University

Suzhou, Jiangsu Province 215123

P. R. China

Tel: (86)-512-65882037, Mobile: (86)-13915550536

Youyong Li's group 

Structure / function prediction and simulation of nanomaterials, polymer materials, and proteins.

 

Education:

PHD, chemistry, California Institute of Technology, 2004

M.S., Chemistry, Peking University, China, 2000

B.S., Chemistry, Peking University (with honor), China, 1997

 

Professional Experience

2009 ~ Present, Professor, Institute of Functional Nano and Soft materials, Soochow University, China

2006 ~ 2009, Director of functional material and biotech, Materials Simulation Center, California Institute of Technology

2004 ~ 2005, Postdoctoral Scholar, California Institute of Technology,

 

Awards

IET Fellowship (1996)

Highest Fellowship of Peking University (1995)

BaoSteel (BaoGang) Fellowship (1995)

Second Prize in Chinese National Chemistry Olympiad (1992)

 

Professional Activities

  Editorial Advisory Board Member of "Current Computer-Aided Drug Design"

 

Current Research Funding

 

 

Patent

US Patent, (WO/2008/097560) “Methods for the Identification of Drugs that Interact with the G Protein Coupled Receptor DP”, Inventors: William A. Goddard III, Nagarajan Vaidehi, Youyong Li, et al.

 

Publications

1.      Soo-Kyung Kim, Youyong Li, Ravinder, Abrol, Jiyoung Heo, William A. Goddard, “Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors”, J. Chem. Inf. Model., 2011, 51, 420-433.

2.      Soo-Kyung Kim, Youyong Li, Changmoon Park, Ravinder, Abrol, William A. Goddard, “Prediction of the 3D structure for the rat urotensin II G-protein-coupled receptor and comparison of the antagonis binding sites and binding selectivity between human and rat from atomistic simulations.” ChemMedChem, 2010, 5， 1594-1608.

3.      Youyong Li, Tingjun Hou, William A Goddard “Computational modeling of structure-function of G protein coupled receptors with applications for drug design.” Current Medicinal Chemistry, 2010, 17, 1167-1180.

4.      Tingjun Hou, Youyong Li, Wei Wang, “Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy”, Bioinformatics, 2011, 27, 1814-1821.

5.      Sheng Tian, Youyong Li, Junmei Wang, Jian Zhang, Tingjun Hou, “ADME Evaluation in Drug Discovery. 9. Prediction of Oral Bioavailability in Human based on Molecular Properties and Structural Fingerprints”, Molecular Pharmaceutics, 2011, 8, 841-851.

6.      Jingyu Zhu, Junmei Wang, Huidong Yu, Youyong Li, and Tingjun Hou, “Recent Developments of In Silico Predictions of Oral Bioavailability.” Combinatorial Chemistry & High Throughput Screening, 2011, 14, 362-374.

7.      Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang, “Assessing the performance of the MM/PBSA and MM/GBSA methods. II. The accuracy of ranking poses generated from docking”, Journal of Computational Chemistry, 2011, 32, 866-877.

8.      Lei Chen, Youyong Li, Qin Zhao, Hui Peng, and Tingjun Hou, “ADME Evaluation in Drug Discovery. 10. Predictions of P-Glycoprotein Inhibitors Using Recursive Partitioning and Naïve Bayesian Classification Techniques.” Molecular Pharmaceutics, 2011, 8, 889-900.

9.      Yang Li, Mingfa Peng, Jing Gao, Qingliang Li, Xuhui Sun and Youyong Li, Gang Yuan, Wen Wen and M. Meyyappan, “Thermal Phase Transformation of In2Se3 Nanowires studied by Synchrotron Radiation X-ray Diffraction and theoretical simulation”, Journal of Materials Chemistry, 2011,21,6944-6947.

10.  Yi Wang, Tingjun Hou, Sheng Tian, Shuit-Tong Lee, Youyong Li, “Influence of doping effect on zinc oxide by first principles studies”, J. Phys. Chem. C, 2011, 115, 7706-7716. 

11.  Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang, “Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations”, 2011, J. Chem. Inf. Model, 51, 69-82.

12.  Youyong Li, Tingjun Hou “Computational simulation of drug delivery at molecular level” Current Medicinal Chemistry, 2010, 4482-4491.

13.  Andres Jaramillo-Botero, Mario Blanco, Youyong Li, Garrett McGuinness, William A Goddard, J. Comput. Theor. Nanosci. 2010, 7, 1238-1256.

14.  William. A. Goddard, Soo.-Kyung. Kim, Youyong Li et al. “Predicted 3D structures for adenosine receptors bound to ligands: Comparison to the crystal structure.”J. Struct. Biol. 2010, 170, 10-20.

15.  Prabal Maiti, Youyong Li, Tahir Cagin, William A Goddard , “Structure of polyamidoamide dendrimers up to limiting generations: A mesoscale description.” J. Chem. Phys. 2009, 130, 144902. 

16.  Tingjun Hou, Youyong Li, Wei Zhang, Junmei Wang, “In silico predictions of intestinal absorption and bioavailability”, Combinatorial Chemistry & High Throughput Screening, 2009, 12, 497-506.

17.  Jun Yang, Mahender B. Dewal, Salvatore Profeta Jr., Mark D. Smith, Youyong Li, and Linda S. Shimizu, "Origins of selectivity for the [2+2] cycloaddition of alpha, beta-unsaturated ketones within a porous self-assembled organic framework." J. Am. Chem. Soc., 2008, 130, 612-621.

18.  Youyong Li, William A. Goddard III, “Prediction of the structure of G-Protein Coupled Receptor with application for drug design” Pacific Symposium on Biocomputing, 2008, 13, 344-353.

19.  Youyong Li, Fangqiang Zhu, Nagarajan Vaidehi, William A. Goddard III, et al. “Prediction of the 3D Structure and dynamics of Human DP G-Protein Coupled Receptor bound to an agonist and an antagonist”, J. Am. Chem. Soc. 2007, 129, 10720 -10731.

20.  Tingjun Hou, Junmei Wang, Youyong Li, “ADME evaluation in drug discovery. 8. The prediction of intestinal absorption by a support vector machine”, Journal of Chemical Information and Modeling, 2007, 47, 2408-2415.

21.  Youyong Li, William A. Goddard III, “Continuous self avoiding walk with application to the description of polymer chains”, J. Phys. Chem. B. 2006, 110, 18134-18137.

22.  Youyong Li, Shiang-Tai Lin, William A. Goddard III, “Efficiency of various lattices from hardball to softball: theoretical study of thermodynamic properties of dendrimer liquid crystal from atomistic simulations”, J. Am. Chem. Soc. 2004, 126, 1872-1885.

23.  Youyong Li, William A. Goddard III, N. S. Murthy, “Crystal structure and properties of N6/AMCC copolymer from theory and fiber XRD”, Macromolecules 2003, 36, 900-907.

24.  Youyong Li, William A. Goddard III, “Nylon 6 Crystal Structures, Folds, and Lamellae from Theory”, Macromolecules 2002, 35, 8440-8455.

25.  Tingjun Hou, Lili Zhu, Youyong Li, et al. “The localization and adsorption of benzene and propylene in ITQ-1 zeolite: grand canonical Monte Carlo simulations”, J. Mol. Struct.-Theo. 2001, 535: 9-23.

26.  Youyong Li, Tingjun Hou, Senli Guo, Xiaojie Xu, “The Mesodyn simulation of pluronic water mixtures using the 'equivalent chain' method”, Phys. Chem. Chem. Phys., 2000, 2, 2749-2753.

27.  Jinfeng Wang, Xinruo Jia, Hong Zhong, Huizhong Wu, Youyong Li, Xiaojie Xu, Mingqian Li, Yen Wei. “Cinnamoyl shell-modified poly(amidoamine) dendrimers” J. Polym. Sci. Pol. Chem. 2000, 38, 4147-4153.

28.  Tingjun Hou, Youyong Li, Yuankang He, et al. “Substituents effect on the optical properties of benzonitrile and oligobenzonitriles” Chinese Chem. Lett. 2000, 11, 693-696.

29.  Tingjun Hou, Youyong Li, Ning Liao, et al. “Three-dimension quantitative structure-activity relationship analysis of some cinnamamides using comparative molecular similarity indices analysis (CoMSIA)” J. Mol. Model. 2000, 6, 438-445.

30.  Tingjun Hou, Junmei Wang, Youyong Li, et al. “Application of genetic algorithm to the QSAR research of pyrrolobenzothiazepinones and pyrrolobenzoxazepinones-novel and specific non-nucleoside HIV-1 reverse transcription inhibitors” Chinese Chem. Lett. 1998, 9, 651-654.

31.  Junmei Wang, Tingjun Hou, Youyong Li, et al. “The QSAR research of pyrrolobenzothiazepinones and pyrrolobenzo-xazepinones - Novel and specific non-nucleoside HIV-1 reverse transcriptase inhibitors” Chinese Chem. Lett. 1997, 8, 889-892.

32.  Youyong Li; Senli Guo; Xiaojie Xu. PROGRESS IN CHEMISTRY, 2000, 12(4), 361.

33.  Youyong Li, Tingjun Hou, Kaixuan Wang, et al. “Theoretical study of the mesoscopic morphology of the pluronics water mixtures” ACTA CHIM SINICA 2000, 58 (4): 402-406.

34.  Zengru Wu, Youyong Li, Xiaojie Xu“Screening of Combinatorial Libraries and Its Application in Drug Discovery” PKU2000-03-20 Vol.36 No.2 pp.275-285.

35.  Tingjun Hou, Yu An, Youyong Li, et al. “Electrostatic interactions in three types of metallothioneins aggregates” ACTA CHIM SINICA 2000, 58 (3): 313-318.

36.  Tingjun Hou, Youyong Li, Yuankang He, et al., Substituent effect on the geometrical structures and electronic properties of benzonitrile oligobenzonitriles, Acta Phys-Chim Sin 2000, 16 (10): 886-891.

37.  Tingjun Hou, Youyong Li, Ning Liao, Xiaojie Xu, “Force field analysis based on genetic algorithm.”, Computational and applied chemistry, 2000, 17, 1-2.

38.  Lirong Chen, Tingjun Hou, Youyong Li, Xiaojie Xu, “Monte Carlo Simulation of Benzene on Y-type zeolite”，Computational and applied chemistry, 2000, 17, 45-46.

39.  Youyong Li, Tingjun Hou, Xiaojie Xu, “Mesocale Simulation of Pluronics polymer”, Computational and applied chemistry, 1999, 16, 365-366.