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欢迎访问精准分子力场与生物信息学课题组
精准分子力场与生物信息学课题组（Precise Force Field and Bioinformatics Laboratory）创立于2007年1月，隶属于上海交通大学微生物代谢国家重点实验室。本课题组致力于计算生物学与生物信息学等学科的方法学研究，并将其应用于探索重要疾病的发生发展的分子机制等领域。代表性的研究工作聚焦于天然无规蛋白的精准分子力场研究，分别发展了基于AMBER、CHARMM以及OPLS的系列力场参数，比如ff99IDPs, ff14IDPs, ff14IDPSFF, ff03CMAP, ESFF1, CHARMM36IDPSFF以及OPLSIDPSFF等。力场参数发表后受到美国加州大学圣地亚哥分校美国科学院院士Andrew McCammon等国内外同行的广泛关注。
新闻
2024 文章接收：
"Graphormer Supervised De Novo Protein Design Method and Function Validation" has been accepted by Briefings in Bioinformatics. 上海交大学术新闻网报道
2023 文章接收：
The paper titled "Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model" has been accepted by J. Chem. Inf. Model. 宇道生物微信公众号报道
2022 文章接收：
The paper titled "Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization." has been accepted by J. Chem. Inf. Model. (doi) 微信公众号报道
2021 文章接收：
The paper titled "Disaggregation mechanism of prion amyloid for tweezer inhibitor" has been accepted by International Journal of Biological Macromolecules . (doi)
The paper titled "Recent Force Field Strategies for Intrinsically Disordered Proteins" has been accepted by J. Chem. Inf. Model. (doi)
2020 文章接收：
The paper titled "Algorithm-based Coevolution Network Identification Reveals Key Functional Sectors of the α/β Hydrolase Subfamilies" has been accepted by The FASEB Journal. (doi)
The paper titled "Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins" has been accepted by J. Chem. Inf. Model. (doi) 微信公众号报道
2019 文章接收：
The paper titled "Well-balanced Force Field ff03CMAP for Folded and Disordered Proteins" has been accepted by J. Chem. Theory Comput. (doi)
The paper titled " Dynamical Important Residue Network (DIRN): Network Inference via Conformational Change" has been accepted by Bioinformatics. (doi) 上海交大学术新闻网报道
2018 文章接收：
The paper titled "Order-Disorder Transition of Intrinsically Disordered Kinase Inducible Transactivation Domain of CREB" has been accepted by J. Chem. Phys.. (doi)
研究方向
1. 天然无规蛋白精准分子力场的研究
天然无规蛋白是一类在生理条件下没有稳定三级结构的蛋白质。这类蛋白在真核生物蛋白质组中的含量超过40%，而且天然无规蛋白与肿瘤、心血管疾病、神经退行性疾病以及糖尿病等复杂疾病的发生发展密切相关。与结构蛋白相比，天然无规蛋白具有构象多样性的特点难于采用X-ray、NMR等传统实验方法来研究。分子力场是模拟天然无规蛋白的基础。而现有的结构蛋白的分子力场不能很好模拟天然无规蛋白。因而，我们从2013年开始分别矫正了八个无规倾向性的氨基酸、二十种氨基酸、八十种氨基酸环境的CMAP参数，发展了基于AMBER、CHARMM以及OPLS的系列精准分子力场，比如ff99IDPs, ff14IDPs, ff14IDPSFF, ff03CMAP, ESFF1, CHARMM36IDPSFF以及OPLSIDPSFF等。测试结果表明，新力场能重现天然无规蛋白的构象特征，并准确预测天然无规蛋白的化学位移、J-Coupling、NOE等参数。力场参数发表之后，收到大量同行的邮件索要力场参数，其中就包括美国科学院院士Andy McCammon等。这些成果将广泛应用于研究天然无规蛋白的结构与功能关系。
2. 计算机辅助创新药物设计
计算机辅助创新药物设计(computer aided innovation drug design)是以分子模型为基础，通过计算机模拟与计算研究药物与受体大分子之间的相互作用，从而设计和优化先导药物的人工智能方法。我们课题组采用三维定量构效关系（3D-QSAR）结合分子对接、分子动力学模拟的方法分别研究了HIV-1蛋白酶、逆转录酶、蛋白整合酶以及CCR5抑制剂，COVID-9，肿瘤等靶标的分子机制，并构建中肯的预测模型。中国经济导报以及云智时代等都报道了我们在抗新冠药物虚拟筛选方面的工作。
3. 蛋白质分子设计
随着生化和结构数据的增长，酶工程正在从随机突变向理性设计发展，而理性设计最重要的一步就是如何获得酶的关键功能氨基酸。通常氨基酸的保守程度可以作为其功能重要的一个判断标准，然而，酶功能也依赖于氨基酸之间的协同作用。共进化指的是在成对的生物个体或者生物分子之间发生的协同变化，通常用来维持或者优化这些生物体或者生物分子之间的功能相关性。蛋白质水平的共进化分析，可以确定蛋白质之间的相互作用位点，进而演化成特定蛋白质亚家族之间共同保守的氨基酸群。统计偶联共进化分析方法可以定位那些对亚家族功能特性相关的氨基酸，比如酶的活性、热稳定性、底物结合特异性等，从而可以用于指导酶进化设计。我们从酶家族序列与结构出发，提出了一种以共进化理论为指导的酶进化设计新方法。（链接）
研究团队
课题组长
陈海峰
教授 精准分子力场与生物信息学课题组 微生物代谢国家重点实验室 生物信息学与生物统计学系 上海交通大学生命科学技术学院 Chem. Biol. Drug Des. 杂志副主编 中国上海市闵行区东川路800号综合实验大楼三号楼512室 邮编：200240 电话：00862134204348 传真：00862134204348 邮箱：haifengchen@sjtu.edu.cn
魏婷
助理研究员 精准分子力场与生物信息学课题组 生物信息学与生物统计学系 上海交通大学生命科学技术学院 中国上海市闵行区东川路800号叶杰全楼511室 邮箱：weitinging@sjtu.edu.cn
学生
陈岳
加入时间：2008.9 专业背景：生物技术 研究方向：分子动力学模拟，药物设计 邮箱：chenyuewillsh@icloud.com
叶纬
加入时间：2010.9 专业背景：生物信息学 研究方向：分子力场的开发与应用，多组学数据分析 邮箱：yw20055968@126.com
杨晶旭
加入时间：2011.9 专业背景：生物信息学 研究方向：分子动力学模拟，别构通路研究及网络分析 邮箱：yangjingxusjtu@163.com
江诚
加入时间：2012.9 专业背景：生物技术 研究方向：核糖开关，分子调控 邮箱：jiang_cheng1990@163.com
张金脉
加入时间：2013.9 专业背景：生物化学与分子生物学 研究方向：分子动力学模拟，基因组分析，基因编辑 邮箱：zhangjinami@sjtu.edu.cn
徐丽诗
加入时间：2013.9 专业背景：生物信息学 研究方向：分子动力学模拟，酶进化 邮箱：laplacecat@hotmail.com
刘灏
加入时间：2014.9 专业背景：生物信息学 研究方向：天然无规蛋白力场的开发与测试 邮箱：haoliu_sjtu@foxmail.com
钱天乐
加入时间：2015.7 专业背景：结构生物学 研究方向：分子动力学模拟，蛋白质结构与功能 邮箱： qiantianle8881@163.com
郭翔
加入时间：2015.9 专业背景：生物信息学 研究方向：力场测试，c-Myb的折叠机制 邮箱： df1992@sjtu.edu.cn
李泉
加入时间：2016.6 专业背景：生物信息学 研究方向：分子动力学模拟，蛋白质别构机制研究，网络分析 邮箱： leejack@sjtu.edu.cn
Ashfaq Ur Rehman
加入时间：2016.9 专业背景：生物化学 研究方向：别构调节机制，自抑制蛋白 邮箱：raysjtu@sjtu.edu.cn
宋东
加入时间：2016.9 专业背景：生物信息学 研究方向：分子力场开发，计算机辅助药物设计 邮箱：dongsong@sjtu.edu.cn
但傲欢
加入时间：2017.8 专业背景：生物化工 研究方向：力场测试，天然无规蛋白的动态模拟 邮箱：danaohuan@sjtu.edu.cn
张阳鹏
加入时间：2017.9 专业背景：生物信息学 研究方向：分子力场开发 邮箱：zhangyp@sjtu.edu.cn
田晓翩
加入时间：2018.9 专业背景：生物信息学 研究方向：分子力场开发 邮箱：tianxp18@sjtu.edu.cn
洪晓昆
加入时间：2020.8 专业背景：生物学 研究方向：组学数据分析及数据库开发 邮箱：hongxk@sjtu.edu.cn
崔晓晨
加入时间：2019.9 专业背景：生物信息学 研究方向：IDP分子力场开发测试 邮箱：cxc_cc@sjtu.edu.cn
陈俊
加入时间：2019.9 专业背景：生物信息学 研究方向：RNA分子力场开发测试 邮箱：0706cj@sjtu.edu.cn
钟博子韬
加入时间：2017.9 专业背景：生物信息学 研究方向：PTM力场开发测试 邮箱：zbztzhz@163.com
季晓悦
加入时间：2020.9 专业背景：生物信息学 研究方向：分子力场开发 邮箱：xiaoyueji@sjtu.edu.cn
蒋雨欣
加入时间：2020.9 专业背景：生物学 研究方向：蛋白质分子设计 邮箱：yuxinjiang0829@163.com
穆俊羲
加入时间：2018.9 专业背景：生物信息 研究方向：全原子水模型开发/蛋白设计/RNA分子力场 邮箱：decoder_mu@sjtu.edu.cn
李政新
加入时间：2020.9 专业背景：生物信息 研究方向：RNA分子力场开发测试 邮箱：lizhengxin@sjtu.edu.cn
宋歌
加入时间：2021.9 专业背景：生物信息 研究方向：磷酸化蛋白分子力场/RNA分子力场 邮箱：calvins@sjtu.edu.cn
张博
加入时间：2021.9 专业背景：生物信息 研究方向：蛋白质设计 邮箱：zhangbo777@sjtu.edu.cn
朱骏杰
加入时间：2021.3 专业背景：生物科学（强基计划） 研究方向：AI辅助增强采样 邮箱：shiroyuki@sjtu.edu.cn
张宁杰
加入时间：2021.8 专业背景：生物信息 研究方向：蛋白质设计 邮箱：ningbao@sjtu.edu.cn
曹玥迪
加入时间：2021.9 专业背景：细胞生物学 研究方向：小分子代谢物 邮箱：caoyuedi@sjtu.edu.cn
郑卓齐
加入时间：2022.09 专业背景：生物制药 研究方向：蛋白设计 邮箱：h2knight@sjtu.edu.cn
崔泰英
加入时间：2021.10 专业背景：生物学 研究方向：RNA分子力场 邮箱：sy19685347@sjtu.edu.cn
刘可欣
加入时间：2022.7 专业背景：生物医学科学 研究方向：蛋白设计 邮箱：lkxlkx@sjtu.edu.cn
林晓倩（博后）
加入时间：2024.02 专业背景：生物医学工程 研究方向：蛋白设计/液-液相分离 邮箱：xqlin@sjtu.edu.cn
余晋宇
加入时间：2023.9 专业背景：计算生物学 研究方向：蛋白设计 邮箱：yujinyu2016@sjtu.edu.cn
孙雨桐
加入时间：2022.9 专业背景：化学 研究方向：修饰RNA分子力场 邮箱：sunyutong@sjtu.edu.cn
返回顶部科研成果
发表文章（代表性）
1. Z. Wu, H. Liu, L. Xu, H.F. Chen*, Y. Feng*. Algorithm-based Coevolution Network Identification Reveals Key Functional Sectors of the α/β Hydrolase Subfamilies. The FASEB Journal. 2020, 34:1983-1995. (IF=5.391)
2. D. Song, H. Liu, R. Luo*, H.F. Chen*. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. J. Chem. Inf. Model. 2020, 60:2257−2267.
3. Y. Zhang, H. Liu, S. Yang, R. Luo*, H.F. Chen*. Well-balanced Force Field ff03CMAP for Folded and Disordered Proteins. J. Chem. Theory Comput. 2019,15:6769-6780. (IF=5.313) (Citation: 1)
4. Q. Li, R. Luo*, H.F. Chen*. Dynamical Important Residue Network (DIRN): Network Inference via Conformational Change. Bioinformatics. 2019, 35:4664-4670.
5. D. Song, R. Luo*, H.F. Chen*. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2017, 57:1166-1178 (Citation: 72).
6. J. Yang, H. Liu, X. Liu, C. Gu, R. Luo, H.F. Chen*. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J. Chem. Inf. Model. 2016, 56: 1184-1192 (Citation: 24).
7. W. Ye, D. Ji, W. Wang, R. Luo, H.F. Chen*. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2015, 55: 1021-1029 (Citation: 34).
8. Z. Li, J. Mu, J. Chen, H.F. Chen*. Base-specific RNA force field improving the dynamics conformation of nucleotide. International Journal of Biological Macromolecules. 2023.222(Pt A):680-690.
9. W. Wang, W. Ye, C. Jiang, R. Luo, H.F. Chen*. New force field on modeling intrinsically disordered proteins. Chem. Biol. Drug Des. 2014, 84: 253-269 (citation: 64).
10. Z. Huang, L. Zhu, Y. Cao, G. Wu, X. Liu, Y. Chen, Q. Wang, T. Shi, Y. Zhao, Y. Wang, W. Li, Y. Li, H.F. Chen*, G. Chen, J. Zhang*. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 2011, 39: D663-D669 (Citation: 103).
11. F. Qin, Y. Chen, M. Wu, Y. X. Li, J. Zhang, H.F. Chen*. Induced Fit or Conformational Selection for RNA/U1A folding. RNA. 2010, 16:1053-1061 (Citation: 40).
12. H.F. Chen*. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J. Chem. Theory Comput. 2008, 4: 1360-1368 (Citation: 34).
13. H.F. Chen, R. Luo*. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129:2930-2937 (Citation: 92).
所有发表文章
129. X. Hong, K. Song, M. Rahman, T. Wei, Y. Zhang, L.Da, H.F. Chen*.Phosphorylation Regulation Mechanism of β2 Integrin for the Binding of Filamin Revealed by Markov State Model. J. Chem. Inf. Model. 2023,63(2):605-618.
128. G. Song, B. Zhong, B. Zhang, A. Rehman, H.F. Chen*.Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. J. Chem. Inf. Model. 2023,63, 5, 1602–1614.
127. X. Hong, N. Li, J. Lv, Y. Zhang, J. Li*, J. Zhang*, H.F. Chen*.PTMint Database of Experimentally Verified PTM Regulation on Protein-Protein Interaction. Bioinformatics. 2023, 39: btac823.
126. X. Ji, H. Liu, Y. Zhang, J. Chen, H.F. Chen*.Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. J. Chem. Inf. Model. 2023,63: 362-374.
125. M. Rahman, K. Song, L. Da*, H.F. Chen*. Early aggregation mechanism of Aβ16-22 revealed by Markov state models. International Journal of Biological Macromolecules. 2022.204:606-616..
124. B. Zhong, G. Song, H.F. Chen*. Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site. International Journal of Molecular Sciences 2022, 23(19), 11285.
123. X. Cui, H. Liu, H.F. Chen*. Polarizable Force Field of Intrinsically Disordered Proteins with CMAP and Reweighting Optimization. J. Chem. Inf. Model. 2022,62, 20, 4970.
122. Z. Li, J. Mu, J. Chen, H.F. Chen*. Base-specific RNA force field improving the dynamics conformation of nucleotide. International Journal of Biological Macromolecules .2022.222(Pt A):680-690.
121. X. Cui , H. Liu, A. Rehman, H.F. Chen*. Extensive evaluation of environment-specific force field for ordered and disordered proteins. Phys. Chem. Chem. Phys 2021. 23, 12127-12136
120. A. Rehman, G. Zheng, B. Zhong, D. Ni, J.Y. Li, H. Rafiq, M. Gabr, A. Nasir, J. Zhang, A. Wadood*, S. Lu*, H.F. Chen*. Mechanism of Zinc Ejection by Disulfiram in Nonstructural Protein 5A. Phys. Chem. Chem. Phys 2021. 23, 12204-12215
119. M. Rahman, A. Rehman, T. Arshad, H.F. Chen*. Disaggregation Mechanism of Prion Amyloid for Tweezer Inhibitor. International Journal of Biological Macromolecules. 2021, 176:510-519
118. J. Mu, H. Liu, J. Zhang*, R. Luo* H.F. Chen*. Recent Force Field Strategies for Intrinsically Disordered Proteins. J. Chem. Inf. Model.2021, 61:1037-1047. (Citation: 1)
117. B. Wu, H. Liu, H. Cai, W. Tao, G. Wang, X. Shi, H.F. Chen*, R. Li*. Vaccine targeting TNF epitope 1-14 do not suppress host defense against Mycobacterium bovis Bacillus Calmette-Guérin infection. International Journal of Biological Macromolecules.2021,169:371-383
116. D. Song, H. Liu, R. Luo*, H.F. Chen*. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. J. Chem. Inf. Model 2020,60:2257-2267. (Citation: 12)
115. A. Rehman, M, Rahman, S. Lu, H. Liu, J.Y. Li, T. Arshad, A. Wadood, H. L. Ng, H.F. Chen*. Decoding Allosteric Communication Pathways in Protein Lysine Acetyltransferase.International Journal of Biological Macromolecules. 2020,147:70-80.
114. Z. Wu, H. Liu, L. Xu, H.F. Chen*,Y. Feng*.Algorithm-based Coevolution Network Identification Reveals Key Functional Sectors of the α/β Hydrolase Subfamilies. The FASEB Journal. 2020,34:1983-1995. (IF=5.391) (Citation: 2)
113. Z. Wu, H. Liu, L. Xu, H.F. Chen*,Y. Feng*. Algorithm-based Coevolution Network Identification Reveals Key Functional Sectors of the α/β Hydrolase Subfamilies. J. Chem. Inf. Model. 2020,7.34:1983-1995. (IF=5.391) (Citation: 2)
112. Y. Zhang,H.F. Chen*. Allosteric Mechanism of an Oximino-piperidino-piperidine Antagonist for the CCR5 Chemokine Receptor. Chem. Biol. Drug Des. . 202095:113-123.
111. Y. Zhang, H. Liu, S. Yang, R. Luo*, H.F. Chen*. Well-balanced Force Field ff03CMAP for Folded and Disordered Proteins. J. Chem. Theory Comput. 2019, 15:6769-6780. (IF=5.313) (Citation: 1)
110. Q. Li, R. Luo*, H.F. Chen*. Dynamical Important Residue Network (DIRN): Network Inference via Conformational Change. Bioinformatics. 2019, 35:4664-4670.
109. Z. Wu, H. Liu, L. Xu, H.F. Chen*, Y. Feng*. Algorithm-based Coevolution Network Identification Reveals Key Functional Sectors of the α/β Hydrolase Subfamilies. The FASEB Journal. 2020, 34:1983-1995. (IF=5.391)
108. D. Song, H. Liu, R. Luo*, H.F. Chen*. Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins. J. Chem. Inf. Model. 2020, 60:2257−2267.
107. A. Rehman, M, Rahman, S. Lu, H. Liu, J.Y. Li, T. Arshad, A. Wadood, H. L. Ng, H.F. Chen*. Decoding Allosteric Communication Pathways in Protein Lysine Acetyltransferase. International Journal of Biological Macromolecules. 2020, 147:70-80.
106. A. Ur Rehman, H. Rafiq, M. Ur Rahman, J. Li, H. Liu, S. Luo, T. Arshad, A. Wadood, H.F. Chen*. Gain-of-Function SHP2 E76Q Mutant Recusing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia. J. Chem. Inf. Model. 2019, 59:3229-3239.
105. A. Ur Rehman, M. T. Khan, H. Liu, A. Wadood, S. I. Malik, H.F. Chen*. Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 of Mycobacterium tuberculosis. J. Chem. Inf. Model. 2019, 59: 1584-1597.
104. S. Yang, H. Liu, Y. Zhang, H. Lu*, H.F. Chen*. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. J. Chem. Inf. Model. 2019, 59:4793-4805.
103. H. Liu, D. Song, Y. Zhang, S. Yang, R. Luo*, H.F. Chen*. Extensive Test and Evaluation of CHARMM36IDPSFF Force Field for Intrinsically Disordered Protein and Folded Protein. Phys. Chem. Chem. Phys. 2019, 21:21918-21931.
102. Y. Zhang, H.F. Chen*. Allosteric Mechanism of an Oximino-piperidino-piperidine Antagonist for the CCR5 Chemokine Receptor. Chem. Biol. Drug Des. 2020, 95:113-123.
101. A. Dan, H.F. Chen*. Secondary structures transition of tau protein with intrinsically disordered proteins specific force field. Chem. Biol. Drug Des. 2019, 93:242–253.
100. A. Ur Rehman, M. Ur Rahman, M. T. Khan, S. Saud, H. Liu, D. Song, P. Sultana, A. Wadood, H.F. Chen*. The Landscape of Protein Tyrosine Phosphatase (Shp2) and Cancer. Current Pharmaceutical Design. 2018, 24: 3767-3777.
99. H. Liu, X. Guo, J. Han, R. Luo*, H.F. Chen*. Order-Disorder Transition of Intrinsically Disordered Kinase Inducible Transactivation Domain of CREB. The Journal of Chemical Physics. 2018, 148:225101.
98. W. Fan, H. Liu, P. Liu, X. Deng, H. F. Chen, Q. Liu, Y. Feng. Characterization of protein interaction surface on fatty acyl selectivity of starter condensation domain in lipopeptide biosynthesis. Applied Microbiology and Biotechnology. 2020, 104: 653–660.
97. Y. Tan, Y. Zhang, Y. Han, H. Liu, H.F. Chen, F. Ma, S. G. Withers, Y. Feng, G. Yang*. Directed evolution of an α1,3-fucosyltransferase using a single-cell ultrahigh-throughput screening method. Science Advances. 2019, 5:eaaw8451.
96. Z. Yang, B. Xu, X. Hu, X. Yao, Y. Tang, C. Qian, S. Wang, H.F. Chen, X. Bai, J. Wu*. Dynein axonemal intermediate chain 2 plays a role in gametogenesis by activation of Stat3. J. Cell Mol. Med. 2019, 23:417-425.
95. L. Zhou, M. Li, X.Y. Wang, H. Liu, S. Sun, H.F.Chen, A. Poplawsky, Y.W. He*. Biosynthesis of Coenzyme Q in the Phytopathogen Xanthomonas campestris via a Yeast-Like Pathway. Mol. Plant Microbe Interact. 2019, 32:217-226.
94. H.X. Jiang, J. Wang, L. Zhou, Z.J. Jin, X.Q. Cao, H. Liu, H.F. Chen, Y.W. He*. Coenzyme Q biosynthesis in the biopesticide Shenqinmycin-producing Pseudomonas aeruginosa strain M18. Journal of Industrial Microbiology & Biotechnology. 2019, 46:1025–1038.
93. L. Feng, C. Chang, D. Song, C. Jiang, Y. Song, C. Wang, W. Deng, Y. Zou, H.F. Chen, X. Xiao, F. Wang, X. Liu*. The trimeric Hef-associated nuclease HAN is a 3’→5’ exonuclease and is probably involved in DNA repair. Nucleic Acids Research. 2018, 46:9027-9043.
92. Y. J. Ye, L. Zhou, X. Liu, H. Liu, D. Li, M. Cao, H.F. Chen, L. Xu, J. Zhu, Y. Zhao*. A novel chemical inhibitor of ABA signaling targets all ABA receptors. Plant Physiol. 2017, 173:2356-2369. (Citation: 0).
91. Q. Li, H.F. Chen*. Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor. RSC Advances. 2018, 8:13067-13074.
90. H. Liu, D. Song, H. Lu*, R. Luo*, H.F. Chen*. Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF. Chem. Biol. Drug Des. 2018, 92:1722-1735. (Cover image + Editor’s choice)
89. D. Song, R. Luo, H.F. Chen*. The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2017, 57:1166-1178 (Citation: 2).
88. W. Ye, T. Qian, H. Liu, R. Luo, H.F. Chen*. Allosteric Autoinhibition Pathway in Transcription Factor ERG: Dynamics Network and Mutant Experimental Evaluations. J. Chem. Inf. Model. 2017, 57:1153-1165 (Citation: 1).
87.Y. Cai, H. Liu, H.F. Chen. Allosteric mechanism of quinoline inhibitors for HIV RT-associated RNase with MD simulation and dynamics fluctuation network. Chem. Biol. Drug Des. 2018, in press.
86. X. Guo, J. Han, R. Luo, H.F. Chen*. Conformation Dynamics of Intrinsically Disordered Protein c-Myb with ff99IDPs Force Field. RSC Advances. 2017, 7:29713 –29721 (Citation: 0).
85. PoH. Liu, W. Ye, H.F. Chen*. Positive Cooperative Regulation of Double Binding Sites for Human Acetylcholinesterase. Chem. Biol. Drug Des. 2017, 89:694-704 (Citation: 0).
84. D. Song, W. Wang, W. Ye, D. Ji, R. Luo, H.F. Chen*. ff14IDPs Force Field Improving the Conformation Sampling of Intrinsically Disordered Proteins. Chem. Biol. Drug Des. 2017, 89:5-15 (Citation: 2).
83. T. Qian, J. Wo, Y. Zhang, Q. Song, G. Feng, R. Luo, S. Lin, G. Wu, H.F. Chen*. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Scientific Reports. 2017, 7:40254 (Citation: 0).
82. J. Zhang, C. Jiang, W. Ye, R. Luo, H.F. Chen*. Allosteric Pathways in Tetrahydrofolate Sensing Riboswitch with Dynamics Correlation Network. Mol. BioSyst. 2017, 13:156 -164 (Citation: 0).
81. Y. J. Ye, L. Zhou, X. Liu, H. Liu, D. Li, M. Cao, H.F. Chen, L. Xu, J. Zhu, Y. Zhao*. A novel chemical inhibitor of ABA signaling targets all ABA receptors. Plant Physiol. 2017, 173:2356-2369. (Citation: 0).
80. M. A. Hoque, Y. Zhang, L. Chen, G. Yang, M. A. Khatun, H.F. Chen, L. Hao, Y. Feng*. Stepwise Loop Insertion Strategy for Active Site Remodeling to Generate Novel Enzyme Functions. ACS Chem. Biol. 2017, 12:1188–1193. (Citation: 0).
79. X. Lv, H. Liu, H.F. Chen, H. Gong*. Coupling between ATP hydrolysis and protein conformational change in maltose transporter. Proteins. 2017, 85:207-220 (Citation: 0).
78. J. Zhang, H. Luo, H. Liu, W. Ye, R. Luo, H.F. Chen*. Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Scientific Reports. 2016, 6: 24587 (Citation: 7).
77. W. Wang, C. Jiang, J. Zhang, W. Ye, R. Luo, H.F. Chen*. Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Scientific Reports. 2016, 6: 31005 (Citation: 1).
76. J. Yang, H. Liu, X. Liu, C. Gu, R. Luo, H.F. Chen*. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J. Chem. Inf. Model. 2016, 56: 1184-1192 (Citation: 7).
75. M. Rahman, H. Liu, A. Wadood, H.F. Chen*. Allosteric Mechanism of Cyclopropylindolobenzazepine Inhibitors for HCV NS5B Rdrp via Dynamics Correlation Network Analysis. Mol. BioSyst. 2016, 12:3280-3293 (Citation: 0).
74. W. Ye, D. Ji, W. Wang, R. Luo, H.F. Chen*. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins. J. Chem. Inf. Model. 2015, 55: 1021-1029 (Citation: 15).
73. D. Ji, W. Ye, H.F. Chen*. Revealing the binding mode between respiratory syncytial virus fusion protein and benzimidazolebased inhibitors. Mol. BioSyst. 2015, 11: 1857-1866 (Citation: 0).
72. L. Xu, W. Ye, C. Jiang, J. Yang, J. Zhang, Y. Feng, R. Luo, H.F. Chen*. Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis. J. Phys. Chem. B. 2015, 119: 2844-2856 (Citation: 2.
71. K. Wu, J. Pang, D. Song, Y. Zhu, C. Wu, T. Shao, H.F. Chen*. Selectivity Mechanism of ATP-Competitive Inhibitors for PKB and PKA. Chem. Biol. Drug Des. 2015, 86:9-18. (Citation: 1).
70. W. Wang, W. Ye, C. Jiang, R. Luo, H.F. Chen*. New force field on modeling intrinsically disordered proteins. Chem. Biol. Drug Des. 2014, 84: 253-269 (citation: 28).
69. Q. Yu, W. Ye, C. Jiang, R. Luo, H.F. Chen*. Specific Recognition Mechanism between RNA and KH3 Domain of Nova-2 Protein. J. Phys. Chem. B. 2014, 118: 12426-12434. (Citation: 1).
68. Q. Yu, W. Ye, W. Wang, H.F. Chen*. Global Conformational Selection and Local Induced Fit for the Recognition between Intrinsic Disordered p53 and CBP. PLoS ONE. 2013, 8:e59627 (Citation: 5).
67. W. Wang, W. Ye, Q. Yu, C. Jiang, J. Zhang, R. Luo, H.F. Chen*. Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. J. Phys. Chem. B. 2013, 117:4912-4923 (Citation: 7).
66. W. Ye, J. Yang, Q. Yu, W. Wang, J. Hancy，R. Luo, H.F. Chen*. Kink Turn sRNA Folding upon L7Ae Binding with Molecular Dynamics Simulation. Phys. Chem. Chem. Phys. 2013, 15:18510-18522 (Citation: 8).
65. S. Ma, W. Ye, D. Ji, H.F. Chen*. Insight into the Binding Mode between HIV-1 Integrase and Pyrimidone Analogue Inhibitors with MD Simulation and 3D-QSAR. Med. Chem. 2013, 9:420-433 (Citation: 0).
64. W. Ye, F. Qin, J. Zhang, R. Luo, H.F. Chen*. Atomistic Mechanism of microRNA Translation Upregulation via Molecular Dynamics Simulations. PLoS ONE. 2012, 7: e43788 (Citation: 7).
63. W. Ye, Y. Chen, W. Wang, Q. Yu, Y. Li, J. Zhang, H.F. Chen*. Insight into the Stability of cross-beta Amyloid Fibril from VEALYL Short Peptide with Molecular Dynamics Simulation. PLoS ONE. 2012, 7: e36382 (Citation: 5).
62. F. Qin, W. Ye, Y. Chen, X. Chen, Y. Li, J. Zhang, H.F. Chen*. Specific Recognition between Intrinsically Disordered LEF and DNA. Phys. Chem. Chem. Phys. 2012, 14: 538-545 (Citation: 13).
61. G. Yan, Y. Chen, Y. Li, H.F. Chen*. Revealing Interaction Mode between HIV-1 Protease and Mannitol Analog Inhibitor. Chem. Biol. Drug Des. 2012, 79:916-925 (Citation: 0).
60. Z. Huang, L. Zhu, Y. Cao, G. Wu, X. Liu, Y. Chen, Q. Wang, T. Shi, Y. Zhao, Y. Wang, W. Li, Y. Li, H.F. Chen*, G. Chen*, J. Zhang*. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 2011, 39: D663-D669 (Citation: 66).
59. F. Qin, Y. Jiang, Y. Chen, M. Wu, G. Yan, W. Ye, Y. X. Li, J. Zhang, H.F. Chen*. Conformational Selection or Induced Fit for Brinker and DNA Recognition. Phys. Chem. Chem. Phys. 2011, 13:1407-1412 (Citation: 18).
58. H. Zhang, F. Qin, W. Ye, Z. Li, S. Ma, Y. Xia, Y. Jiang, J. Zhu, Y. Li, J. Zhang, H.F. Chen*. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem. Biol. Drug. Des. 2011, 78:427-437 (Citation: 5).
57. J. Xiong, H. Wang, G. Guo, S. Wang, L. He, H.F. Chen*, J. Wu. Male Germ Cell Apoptosis and Epigenetic Histone Modification Induced by Tripterygium wilfordii Hook F. PLoS ONE. 2011, 6: e20751 (Citation: 11).
56. Z. Li, H. Zhang, Y. Li, J. Zhang, H.F. Chen*. Drug Resistant Mechanism of Diaryltriazine Analog Inhibitors of HIV-1 Reverse Transcriptase Using Molecular Dynamics Simulation and 3D-QSAR. Chem. Biol. Drug. Des. 2011, 77:63-74 (Citation: 4).
55. F. Qin, Y. Chen, M. Wu, Y. X. Li, J. Zhang, H.F. Chen*. Induced Fit or Conformational Selection for RNA/U1A folding. RNA. 2010, 16:1053-1061 (Citation: 32).
54. Y. Chen, Y.J. He, M. Wu, G. Yan, Y.X. Li, J. Zhang, H.F. Chen*. Insight into the Stability of Cross-β Amyloid Fibril from Molecular Dynamics Simulation. Biopolymers. 2010, 93: 578-586 (Citation: 19).
53. Y. Chen, Z. Li , H.F. Chen*. Computational Study of CCR5 Antagonist with Support Vector Machines and Three Dimensional Quantitative Structure Activity Relationship Methods. Chem. Biol. Drug. Des. 2010, 75: 295-309 (Citation: 6).
52. H.F. Chen*. Aggregation Mechanism Investigation of the GIFQINS cross-Amyloid Fibril. Comput. Bio. Chem. 2009, 33: 41-45 (Citation: 18).
51. H.F. Chen*. In Silico logP Prediction for a Large Data Set with Support Vector Machines, Radial Basis Neural Networks and Multiple Linear Regression. Chem. Biol. Drug. Des. 2009, 74: 142-147 (Citation: 6).
50. H.F. Chen*. Post-translational Modification of Phosphorylated KID from Molecular Dynamics Simulation. PLoS ONE. 2009, 4: e6516 (Citation: 37).
49. F. Qin, Y. Chen, Y. X. Li, H.F. Chen*. Induced Fit of mRNA/TIS11d Complex. J. Chem. Phys. 2009, 131: 115103 (Citation: 23).
73. H.F. Chen*. Mechanism of Coupled Folding and Binding in the siRNA-PAZ Complex. J. Chem. Theory Comput. 2008, 4: 1360-1368 (Citation: 29).
48. H.F. Chen*. Quantitative predictions of gas chromatography retention indexes with support vector machines, radial basis neural networks and multiple linear regression. Anal. Chim. Acta. 2008, 609:24-36 (Citation: 26).
47. H.F. Chen*. Computational study of histamine H3-receptor antagonist with support vector machines and three dimension quantitative structure activity relationship methods. Anal. Chim. Acta. 2008, 624:203-209 (Citation: 10).
46. H.F. Chen*. Computational Study of the Binding Mode of Epidermal Growth Factor Receptor Kinase Inhibitors. Chem. Biol. Drug. Des. 2008, 71:434-446 (Citation: 12).
45. Z. Li, J. Han, H.F. Chen*. Revealing Interaction Mode between HIV-1 Reverse Transcriptase and Diaryltriazine Analog Inhibitor. Chem. Biol. Drug. Des. 2008, 72:350-359 (Citation: 8).
44. H.F. Chen*, M.Y. Wu, Z. Wang, D.Q. Wei. Insight into the Metabolism Rate of Quinone Analogues from Molecular Dynamics Simulation and 3D-QSMR Methods. Chem. Biol. Drug. Des. 2007, 70:290-301 (Citation: 4).
43. H.F. Chen, R. Luo*. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129:2930-2937 (Citation: 80).
42. Z. Wang, J. Zhang, H. Li, J. Li, M. Niimi, G. Ding, H.F. Chen, J. Xu, H. Zhang, Z. Xu, Y. Dai, T. Gui, S. Li, Z. Liu, S. Wu, M. Cao, L. Zhou, X. Lu, J. Wang, J. Yang, Y. Fu, D. Yang, J. Song, T. Zhu, S. Li, B. Ning, Z. Wang, T. Koike, M. Shiomi, E. Liu, L. Chen, J. Fan, Y. E. Chen, Y. Li*. Hyperlipidemia-associated gene variations and expression patterns revealed by whole-genome and transcriptome sequencing of rabbit models. Scientific Reports. 2016, 6:26942 (Citation: 0).
41. L. Dong, Q. Tan, W. Ye, D. Liu, H.F. Chen, H. Hu, D. Wen,Y. Liu, Y. Cao, J. Kang, J. Fan, W. Guo, W. Wu*. Screening and Identifying a Novel ssDNA Aptamer against Alphafetoprotein Using CE-SELEX. Scientific Reports. 2015, 5:15552 (Citation: 5).
40. Y. Zhang，J. An，G.Y. Yang，A. Bai，B. Zheng，Z. Lou，G. Wu，W. Ye，H.F. Chen, Y. Feng*, G. Manco. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426. PLos ONE. 2015, 10:e0115130 (Citation: 2 ).
39. J. Gao，X. Luo*，Y. Li，R. Gao，H.F. Chen, D. Ji. Synthesis and Biological Evaluation of 2-oxo-pyrazine-3-carboxamide-yl Nucleoside Analogues and Their Epimers as Inhibitors of Influenza A Viruses. Chem. Biol. Drug. Des. 2015, 85:245-252 (Citation: 2).
38. H. Zhang, Z. Liu, Y. Sun, J. Zhu, S. Lu, X. Liu, Q. Huang,Y. Xie, H. Zhu, S. Dang, H.F. Chen, G. Zheng, Y. Li, Y. Kuang, J. Fei, S. Chen, Z. Chen, Z.G. Wang*. Rig-I regulates NF-κB activity through binding to Nf-κb13′-UTR mRNA. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:6459-6464 (Citation: 10).
37. H. Gu，H.F. Chen, D.Q. Wei, J.F. Wang*. Molecular dynamics simulations exploring drug resistance in HIV-1 proteases. Chinese Science Bulletin. 2010, 55:2677-2683 (Citation: 13).
36. J. Wang, C. Tan, H.F. Chen, R. Luo*. All-Atom Computer Simulations of Amyloid Fibrils Disaggregation. Biophys. J. 2008, 95:5037-5047 (Citation: 22).
35. C.F. Wang, H.Q. Zheng, H.C. Wei, R. Zhang, H.F. Chen, D.Q. Wei. Structure and vibrational frequencies of Ph3PCl2 with discrete solvent molecules and in gas phase. J. Theor. Comput. Chem. 2007, 6:511-521 (Citation: 0).
34. T. Zhang, X. C. Dong, H.F. Chen, M. B. Chen. Docking Study on the Binding Modes of Sulfonylurea Analogues to ALS/AHAS and Virtual Screen of Novel Inhibitors. Acta Chimica Sinica. 2006, 64: 899-905. .
33. H.F. Chen, B.T. Fan*, C.Y. Zhao, L. Xie, C.H. Zhao, T. Zhou, K. H. Lee, G. Allaway. Computational Studies and Drug Design for HIV-1 Reverse Transcriptase Inhibitors of 3’,4’-di-O-(S)-dicamphanoyl-(+)-cis-Khellactone (DCK) Analogs. J. Comput. Aided Mol. Des. 2005, 19:243-258 (Citation: 12)..
32. Q. Zhu, J. H.Yao, S. G. Yuan*, F. Li, H.F. Chen, W. Cai, Q. Liao. Superstructure Searching Algorithm for Generic Reaction Retrieval. J. Chem. Inf. Model. 2005, 45:1214-1222.
31. C.Y. Zhao, G. Dodin, C.S. Yuan, H.F. Chen, R.L. Zheng, Z.J. Jia, B.T. Fan*. ‘In vitro’ protection of DNA from Fenton reaction by plant polyphenol verbascoside. Biochim. Biophys. Acta. 2005, 1723:114-123 (Citation: 49).
30. B.T. Fan, H.F. Chen, H.R. Xia, M. Petitjean, S.G. Yuan, A. Panaye, J. P. Doucet*. New Strategy of Mass Spectrum Simulation Based on Reduced and Concentrated Knowledge Databases. Spectroscopy Lett. 2005, 38:145-170 (Citation: 8).
29. X.J. Yao, A. Panaye, J.P. Doucet, H.F. Chen, R.S. Zhang, B.T. Fan*, M.C. Liu, Z.D. Hu. Comparative classification study of toxicity mechanisms using support vector machines and radial basis function neural networks. Anal. Chim. Acta. 2005, 535: 259-273 (Citation: 54).
28. X.J. Yao, A. Panaye, J.P. Doucet, R.S. Zhang, H.F. Chen, M.C. Liu, Z.D. Hu, B.T. Fan*. Comparative study of QSAR/QSPR correlations using support vector machines, radial basis function neural networks, and multiple linear regression. J. Chem. Inf. Model. 2004, 44:1257-1266 (Citation: 148).
27. H.F. Chen, Q. Li, X.J. Yao, B.T. Fan*, S.G. Yuan, A. Panaye, J.P. Doucet. CoMFA/CoMSIA/HQSAR and Docking Study of the Binding Mode of Selective Cyclooxygenase (COX-2) Inhibitors. QSAR Comb. Sci. 2004, 23:36-55 (Citation: 22).
26. H.F. Chen, X.J. Yao, M. Petitjean, H.R. Xia, J.H. Yao, A. Panaye, J. P. Doucet, B.T. Fan*. Insight into the Bioactivity and Metabolism of Human Glucagon Receptor Antagonists from 3D-QSAR Analyses. QSAR Comb. Sci. 2004, 23:603-620 (Citation: 8).
25. H.F. Chen, J.H. Yao, J. Sun, Q. Li, F. Li, B.T. Fan, S.G. Yuan*. Discovery of anti-SARS Coronavirus Drug Based on Molecular Docking and Database Screening. Chinese Journal of Chemistry. 2004, 22:882-887..
24. Q. Zhu, J.H. Yao，F. Li, H.F. Chen, S.G. Yuan*. Comparison the similarity of R group. Acta Chimica Sinica. 2004, 62:1585-1589.
23. Q. Zhu, J.H. Yao，F. Li, H.F. Chen, S.G. Yuan*. The new method for the classification of reaction data and reaction knowledge. Acta Chimica Sinica. 2004, 62:112-119.
22. H.F. Chen, X.J. Yao, Q. Li, S.G. Yuan, A. Panaye, J. P. Doucet, B.T. Fan*. Comparative Study of Non Nucleoside Inhibitors with HIV-1 Reverse Transcriptase Based on 3D-QSAR and Docking. SAR and QSAR in Environ. Res. 2003, 14:455-474 (Citation: 24).
21. H.F. Chen, Q. Li, X.J. Yao, B.T. Fan*, S.G. Yuan, A. Panaye, J. P. Doucet. 3D-QSAR and Docking Study of the Binding Mode of Steroids to Progesterone Receptor in Active Site. QSAR Comb. Sci. 2003, 22:604-613 (Citation: 17).
20. H.F. Chen, X.C. Dong, B.S. Zeng, K. Gao, S.G. Yuan, A. Panaye, J. P. Doucet, B.T. Fan*. Virtual Screening and Rational Drug Design Method Using Structure Generation System Based on 3D-QSAR and Docking. SAR and QSAR in Environ. Res. 2003, 14:251-264 (Citation: 5).
19. H.F. Chen, B.T. Fan*, H.R. Xia, M. Petitjean, S.G. Yuan, A. Panaye, J. P. Doucet. MASSIS: A Mass Spectra Simulation System 1. Principal and Method. Eur. J. Mass Spectrom. 2003, 9:175-186 (Citation: 6).
18. H.F. Chen, B.T. Fan*, F. Li, M. Petitjean, H.R. Xia, S.G. Yuan, A. Panaye, J. P. Doucet. MASSIS: A Mass Spectra Simulation System 2. Procedures and Performance. Eur. J. Mass Spectrom. 2003, 9:445-457 (Citation: 3).
17. H.F. Chen, J.H. Kang, Q. Li, B. S. Zeng, X. J. Yao, B. T. Fan, S.G. Yuan*. A. Panaye, J.P. Doucet. 3D-QSAR Study on Apicidin Inhibit Histone Deacetylase. Chinese Journal of Chemistry. 2003, 21:1596-1607.
16. B.S. Hayat, H.F. Chen, S.G. Yuan, R. Wen*. 3D-QSAR Study on Diindolylmethane and Its Analogues with Comparative MolecularField Analysis (CoMFA). Chinese Journal of Chemistry. 2003, 21:20-24.
15. J.H. Kang, Y.T. Zhang, J. Chen, H.F. Chen, C. J. Lin, Q. Wang, Y.X. Ou*. Nickel-induced Histone Hypoacetylation: the Role of Reactive Oxygen Species. Toxicol Sci. 2003, 74:279-286.
14. H.F. Chen, K. Gao, B.T. Fan, S.G. Yuan*, Z.J. Jia, R.L. Zheng. A. Panaye, J.P. Doucet. Virtual Screening and Rational Design of Phenylpropanoid Glycosides Analogues Based on Molecular Docking. Acta Chimica Sinica. 2002, 60:1860-1866.
13. J.H. Yao, F. Li, S.W. Luo, S.G. Yuan, H.F. Chen, Q. Li, C.Z. Zheng. Automatic Identification of Tautomeric, Alternating and Aromatic Bonds in Chemical Structures. Acta Chimica Sinica. 2002, 60, 1291-1297.
12. H.F. Chen, Q. Li, B. S. Zeng, X.C. Dong, S.G. Yuan*, M.B. Chen, C.Z. Zheng, R.S. Sun, T.M. Cheng, Y.P. Shu, R.Q. Liu. 3D-QSAR Study on Anti-mast Cell Degranulation of Isoquinoline Compounds. Acta Chimica Sinica. 2001, 59:2143-2147.
11. H.F. Chen, X.C. Dong, Y. Gu, G.Q. Chai, S.X. Zhang, S.G. Yuan*, M.B. Chen, C.Z. Zheng. Study on Anti-Gibberella Fluorine-Containing Pesticides by 3D-QSAR. Acta Chimica Sinica. 2000, 58:1074-1078.
10. Y. Gu, X.C. Dong, H.F. Chen, M.B. Chen*, S.X. Zhang, S.G. Yuan, C.Z. Zheng. 3D-QSAR Study of Flurine-Containing Pesticides. Acta Chimica Sinica. 2000, 58:1540-1545.
9. Y. Gu, M.B. Chen*, X.C. Dong, H.F. Chen, B.S. Zeng, C.L. Feng, B.Yu, Y.Z. Hui. 3D-QSAR Studies of Saponins. Acta Chimica Sinica. 2000, 58:1534-1539.
8. H.F. Chen, J.F. Li, J.H. Yao, S.G. Yuan*, C.Z. Zheng. Automatic Generation of Virtual Bio-Active Compounds. Acta Chimica Sinica. 2000, 58:529-532.
7. H.F. Chen, Y. Gu, X.C. Dong, J.F. Li, S.X. Zhang, S.G. Yuan*, M.B. Chen, C.Z. Zheng. A New Method for De Novo Bio-Active Molecular Design. Acta Chimica Sinica. 2000, 58:1168-1172.
6. H.F. Chen, S.G. Yuan*, S.W. Luo, X.C. Dong, J.H. Yao, S. Yang, C.Z. Zheng. Design of New HIV-1 Protease Inhibitors by Pharmacophore Searching. Acta Chimica Sinica. 2000, 58:287-292.
5. S.G. Yuan*, S.W. Luo, G.Q. Chai, J.H. Yao, H.F. Chen, C.Z. Zheng. From Pharmacophore to Leads: Bioactive Compound Discovery via Computer-aided Techniques. Chinese Journal of Chemistry. 1999, 17:237-243.
4. H.F. Chen, J.H. Yao, S.G. Yuan*, J. F. Li, S. Yang, C. Z. Zheng, B. T. Fan, A. Panaye, J. P. Doucet. Conformationally Flexible Searching in 3D Structure Searching System. Comput. & Appl. Chem. 1999, 16:101-104.
3. S.G. Yuan, J. H. Yao, H.F. Chen, C.Z. Zheng. Building up General Design of 3D Structure Searching System. Comput. & Appl. Chem. 1999, 15:77-80.
2. J.H. Yao, S.G. Yuan, H.F. Chen, C.Z. Zheng, S. Yang, B.T. Fan, A. Panaye, J. P. Doucet. Structure Indexing and Matching in 3D Structure Searching System. Comput. & Appl. Chem. 1999, 16:97-100.
1. S.G. Yuan, H.F. Chen, J. Xu, W.P. Xing, J.H. Yao, C.Z. Zheng. A New Definition of Molecular Similarity Based on Semantic Relation of 3D Structures. Comput. & Appl. Chem. 1999, 16:403-410.
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