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機器學習

王林聰

基本情況
姓名: 王林聰
性别:
職稱: 教授
最高學曆: 研究生
最高學位: 博士
詳細情況
所在學科專業: 生物信息學
所研究方向: 基于結構的藥物設計,計算分子生物學
講授課程: 計算分子生物學
教育經曆: 1986-1990 浙江大學,生命學院,本科/學士
1998年5月于 Michigan State University生物化學系獲博士學位。
1999-2001 the University of Maryland, Department of Computer Science, College Park, MD, USA. Master Program.
工作經曆: 1998-2000在密歇根大學(The University of Michigan)生物物理研究部 (Biophysics Research Division)跟國際著名核磁共振專家 Prof. Erik R. Zuiderweg 做博士後研究。
2001-2006 加入達特茅斯學院 (Dartmouth College)計算機系做研究助理教授。與國際著名人工智能專家和 計算結構生物學專家,ACM Fellow, Prof. Bruce R. Donald 共事。
2006-2007。在新澤西州立大學 (Rutgers University )高等生物科技與醫藥研究中心研究(CABM)做研究助理教授。與國際著名結構生物學專家 Prof. Guy Montelione 共事。
2007-2010。在勃林格-殷格翰(Boehringer Ingelheim)公司藥物化學部結構研究組工作。主要研發項目是小分子藥物跟蛋白質對接算法的設計、實施和分析, 特别是用高通量的但沒有歸屬的NMR數據來确定配體的模式的算法。期間研發了一套使用高通量實驗數據準确地計算對接模式(docking pose)的計算平台。
科研項目: 1. 美國NIH 基金項目 NIH-R01-GM65982 (申請者王林聰是主要參與者)
項目經費: 120 萬美元。
項目名稱: NMR信号自動歸屬和高通量蛋白質結構。
2. 美國NSF 基金項目 EIA-030544 (申請者王林聰是項目主要參與者)
項目經費: 30 萬美元。
項目名稱:計算生物學中的算法挑戰。
3. 美國NSF 基金項目 EIA-9802068 (申請者王林聰是項目共同主持人)
項目經費: 12 萬美元。
項目名稱: 物理幾何算法(Physical Geometric Algorithms)和高通量NMR結構生物學。
學術論文: • 計算機科學會議論文 (conference paper)
[1]. S. Xu, S. Zou and L. Wang A Geometric Clustering Algorithm and Its Applications to Structural Data. (RECOMB2014) (acceptance rate 16.7%, RECOMB is one of the most prestigious conferences in computational biology and bioinformatics).
[2]. L. Wang (2010) The Geometric and Electrostatic Properties of Binding Cavities and Their Usage in Protein-Ligand Docking. Frontier of Computer Science and Technology, Changchun, China (August 2010) pp. 442–447.
[3]. L. Wang and B. R. Donald (2006) A Data-Driven, Systematic Search Algorithm for Structure Determination of Denatured or Disordered Proteins. The Computational Systems Bioinformatics Conference (CSB), Stanford CA (August, 2006) pp. 67–78 (Best Paper Award)。
[4]. L. Wang and B. R. Donald (2005). An Efficient and Accurate Algorithm for Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library Ensemble and Residual Dipolar Couplings. IEEE Computer Society Bioinformatics Conference (CSB2005), Stanford CA (August, 2005) pp. 189–202。
[5]. L. Wang, R. Mettu and B. R. Donald (2005). An Algebraic Geometry Approach to Backbone Structure Determination from NMR Data. IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference (CSB2005) Stanford CA (August, 2005) pp. 235–246。
[6]. L. Wang and B. R. Donald (2004). Analysis of a Systematic Search-Based Algorithm for Determining Protein Backbone Structure from a Minimal Number of Residual Dipolar Couplings. The IEEE Computational Systems Bioinformatics Conference (CSB2004), Stanford CA (August, 2004) pp. 319-330。
[7]. C. Langmead, A. Yan, R. Lilien, L. Wang and B. R. Donald (2003). A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proceedings of the Seventh Annual InternationalConference on Research in Computational Molecular Biology (RECOMB2003), 176-187. Berlin, Germany, April 10-13。
[8]. L. Wang, R. Mettu, R. Lilien and B. R. Donald (2003). An Exact Algorithm for Determining Protein Backbone Structure from NH Residual Dipolar Couplings. IEEE Computer Society Bioinformatics Conference (CSB2003), 611-612. Stanford, CA, August 11-14. (Best Poster Award)。
• 雜志論文 (生物化學,生物物理,結構生物學和計算機科學)
[1]. L. Wang, Y, Hou, H. Quan, W. Xu, Y. Bao, Y. Li, Y. Fu, S. Zou (2013) A Compound-Based Computational Approach for the Accurate Determination of Hot Spots. Protein Science 22(8):1060-70.
[2]. X. Y. Yuan, D. Y. Fu, X. F. Ren, X. Fang, L. Wang, S. Zou, and Y. Wu (2013) Highly Selective Aza-nitrile Inhibitors for Cathepsin K, Structural Optimization and Molecular Modeling. Org. Biomol. Chem. 11(35):5847-5.
[3]. X. F. Ren, H, W. Li, X. Fang, Y. Wu, L. Wang, and S. Zou (2013) Highly Selective Azadipeptide Nitrile Inhibitors for cathepsin K: Design, Synthesis and Activity Assays. Org. Biomol. Chem. 11(7):43-8.
[4]. L. Wang, S. Zou, and Y. Wang (2012) Algorithmic challenges in structure-based drug design and NMR structural biology. Front. Electr. Electron. Eng. 7(1):69-84.
[5]. J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, P. Zhou, and B. R. Donald (2009) High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solution to the RDC Equations. J. Biomol. NMR, 45(3):265-281.
[6]. L. Wang, P. Rossi, C, X. Chen, C. Nwosu, K. Cunningham, L .C. Ma, R. Xiao, J. Liu, M. .C. Baran, G. .T. V. Swapna, T. .B. Acton, R. Burkhard, and G. T. Montelione (2007). Northeast Structural Genomics Consortium Target SiR5 (PDBID 2OA4), RCSB.
[7]. L. Wang, P. Rossi, C. .X. Chen, C. Nwosu, K. Cunningham, L .C. Ma, R. Xiao, J. Liu, M. .C. Baran, G. .T. V. Swapna, T. .B. Acton, R. Burkhard, and G. T. Montelione (2007). Northeast Structural Genomics Consortium Target RHR5 (PDBID 2JRT), RCSB.
[8]. L. Wang and W. Hu (2006) Residual Dipolar Couplings: Measurements and applications to biomolecular studies. Annual Reports on NMR Spectroscopy, 58: 232–304。
[9]. L. Wang, R. Mettu and B. R. Donald (2006). A Polynomial-time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data. Journal of Computational Biology 13(7):1276-1288。
[10]. L. Wang and B. R. Donald (2004) Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and Their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure. J. Biomol. NMR, 29(3):223–242。
[11]. C. Langmead, A. Yan, R. Lilien, L. Wang and B. R. Donald (2003). A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Journal of Computational Biology 11(2–3):277–298。
[12]. L. Wang, Y. Pang, T.Holder, J. R. Brender, A. V. Kurochkin, and E. R. P. Zuiderweg (2001) Functional Dynamics in the Active Site of the Ribonuclease Binase. Proceedings of the National Academy of Sciences, USA, 98,7684–7689。
[13]. L. Wang, A. V. Kurochkin and E. R. P. Zuiderweg (2000) An Iterative Fitting Procedure for the Determination of Longitudinal NMR Cross-Correlation Rates. J. Magn. Reson. 144,175-185。
[14]. M. Pellecchia, Y. Pang, L.Wang, A. V. Kurochkin, A. Kumar and E. R. P. Zuiderweg (1999) Quantitative Measurement of Cross-Correlations Between 15N and 13CO Chemical Shift Anisotropy Relaxation Mechanisms by Multiple Quantum NMR. J. Am. Chem. Soc. 121, 9165-9170。
[15]. Y. Pang, L. Wang, M. Pellecchia, A. V. Kurochkin and E. R. P. Zuiderweg (1999) Evidence for Extensive Anisotropic Local Motions in a Small Enzyme Using a New Method to Determine NMR Cross-Correlated Relaxation Rates in the Absence of Resolved Scalar Coupling. J. Biomol. NMR 14(4), 297-306。
[16]. L. Wang and H. Yan (1999) NMR Studies of Type II Human Cellular Retinoic Acid Binding Protein. Biochimica et Biophysica Acta 1433, 240-252。
[17]. L. Wang, Y. Li, F. Abildgaard, J. L. Markley and H. Yan (1998) NMR Solution Structure of Type II Human Cellular Retinoic Acid Binding Protein: Implications for Ligand Binding. Biochemistry 37, 12727-12736。
[18]. L. Wang and H. Yan (1998) NMR Study Suggests a Major Role for Arg111 in Maintaining the Structure and Dynamical Properties of Type II Cellular Retinoic Acid Binding protein. Biochemistry 37. 13021-13032。
[19]. X. Chen, M. Tordova, G. L. Gilliland, L. Wang, Y. Li, H. Yan and X. Ji (1998) Crystal Structure of Cellular Retinoic Acid Binding Protein Type II: Suggestions a Mechanism of Ligand Entry. J. Mol. Biol. 278, 641-653。
[20]. H. Yan, L. Wang and Y. Li (1997) A Novel Method for Measuring the Binding Properties of the Site-Directed Mutants of The Proteins that Binding Hydrophobic Ligands: Application to Cellular Retinoic Acid Binding Proteins. In Techniques in Protein Chemistry VIII (Marshak D. R. Ed.), 449-456. Academic Press, San Diego。
[21]. L. Wang, Y. Li and H. Yan (1997) Human Cellular Retinoic Acid Binding Proteins: Quantitative Analysis of the Ligand Binding Properties of the Wild-Type and Site-Directed Mutants. J. Biol. Chem. 272, 1541-1547。
獲獎情況: 最佳論文 (Best Paper) 獎,The Computational Systems Bioinformatics Conference (CSB 2006),由IEEE計算機學會與美國電腦協會(ACM)聯和發起。
最佳會議展闆(Best Poster) 獎,The Computational Systems Bioinformatics Conference (CSB 2003),由IEEE計算機學會與美國電腦協會(ACM)聯合發起。
研究獎學金 (Research Fellowship),密歇根州立大學。
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