计算机辅助药物设计(computer aided 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。并结合本课题组开发的精准分子力场发展了药物的虚拟筛选流程,为药物研发奠定方法学基础。
计算机辅助药物设计(computer aided 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。并结合本课题组开发的精准分子力场发展了药物的虚拟筛选流程,为药物研发奠定方法学基础。
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.
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.
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: 151).
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: 156).
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.
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.
J.J. Zhu, Z. Li, H. Tong, Z. Lu, N. Zhang, T. Wei*, H.F. Chen*. Phanto-IDP: Compact Model for Precise Intrinsically Disordered Protein Backbone Generation and Enhanced Sampling. Brief. Bioinformatics. 2024, 25: bbad429.
Z. Pan, J. Mu, H.F. Chen*. Balanced Three-point Water Model OPC3-B for Intrinsically Disordered and Ordered Proteins. J. Chem. Theory Comput. 2023, 19: 4837-4850.