基于Discovery Studio分子模拟药物设计软件的拉伸分子动力学
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摘要
Discovery Studio是BIOVIA公司研发的一款药物发现计算模拟平台。在Discovery Studio 2017中新增拉伸分子动力学模块,拉伸分子动力学模块的功能包括研究配体(药物分子)与受体的结合方式、蛋白质的去折叠构象变化、拉伸配体(药物分子)通过通道蛋白等。本文介绍Discovery Studio 2017的拉伸分子动力学功能。
Discovery Studio is BIOVIA company research and development of a drug discovery and biological macromolecule simulation platform, the new extension molecular dynamics module in Discovery Studio 2017. The function of the steered molecular dynamics module functions include the study of the binding of ligands and receptors, the transformation of proteins to fold the conformation, and the stretching ligands through the channel proteins. This paper introduces the steered molecular dynamics function of Discovery Studio 2017.
Discovery Studio is BIOVIA company research and development of a drug discovery and biological macromolecule simulation platform, the new extension molecular dynamics module in Discovery Studio 2017. The function of the steered molecular dynamics module functions include the study of the binding of ligands and receptors, the transformation of proteins to fold the conformation, and the stretching ligands through the channel proteins. This paper introduces the steered molecular dynamics function of Discovery Studio 2017.
引文
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[2]Paci E,Karplus M.Unfolding Proteins by External Forces and Temperature:The Importance of Topology and Energetics[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(12):6521-6526.
[3]王浩,徐利楠,孙玉娜,等.Ydj1p二聚体中β14~β15与domain-Ⅲ分离的拉伸分子动力学模拟研究[J].生物信息学,2013,11(3):167-171.
[4]Wang Y,Cai W S,Chen L,et al.Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth[J].Oncotarget,2011,8(7).
[5]季海涛,张万年,周有骏,等.药物化学计算机辅助教学方法的建立与应用[J].中国医学教育技术,2002,16(3):169-170.
[6]Paci E,Caflisch A,Plückthun A,et al.Forces and energetics of hapten-antibody dissociation:a biased molecular dynamics simulation study[J].Journal of Molecular Biology,2001,314(3):589-605.
[7]Boyce,S.E.;Mobley D.L.;Rocklin G.J.;et al.Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site[J].J.Mol.Biol,2009,394,747-763.
[8]周雷,徐利楠,周小红,等.Hsc70-Auxilin复合物的拉伸分子动力学模拟[J].生物信息学,2014(2):110-116.
[9]Bavi N,Bavi O,Vossoughi M,et al.Nanomechanical properties of Msc L alpha helices:A steered molecular dynamics study[J].Channels,2016,11(3).
[10]Park M S.Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1[J].Plos One,2015,10(4):e0125361.