在包括J.Am.Chem.Soc, Macromolecules, J. Phys. Chem. B等國際著名期刊上共發表學術論文90餘篇。在研製新的計算模擬算法中,成功發展了自由能計算方法,並套用於複雜體系,如樹枝狀聚合物的液晶結構,闡釋了軟材料聚集過程中焓和熵的分別影響,奠定了軟材料的堆積原理。並成功發展了蒙特卡洛方法,被廣泛套用於預測蛋白質結構的摺疊部分以及聚合物,樹枝狀聚合物的結構。在計算機輔助藥物設計研究中,發展成熟了GPCR的結構預測與藥物設計方法,並與多家國際知名製藥公司進行緊密合作,分別與Pfizer, Sanofi-Aventis, Boerhinger-Ingelhem, Accelerator等合作出多個靶體的活性化合物,其中與Sanofi-Aventis公司合作出活性化合物並進入了臨床實驗。
代表性論文
1. Youyong Li, Tingjun Hou, William A. Goddard III, Molecular modeling of structure-function of G Protein-Coupled Receptors with applications for drug design, Current Medicinal Chemistry, 2009, (invited review, in press)
2. Prabal Maiti, Youyong Li, Tahir Cagin, William A Goddard III, Structure of PAMAM dendrimers upt to limiting generations: A mesoscale description, J. Chem. Phys. 2009, In press.
3. 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.
4. 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 (35), 10720 -10731.
5. 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.
6. Tingjun Hou, Youyong Li, Wei Zhang, Junmei Wang, In silico predictions of intestinal absorption and bioavailability, Combinatorial Chemistry & High Throughput Screening, (invited review, in press)
7. 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.
8. 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.
9. 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.
10. Youyong Li, William A. Goddard III, Nylon 6 Crystal Structures, Folds, and Lamellae from Theory, Macromolecules 2002, 35, 8440-8455.
11. 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 (12): 2749-2753.