大学化学 >> 2018, Vol. 33 >> Issue (5): 66-71.doi: 10.3866/PKU.DXHX201801023

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Schrödinger药物虚拟筛选流程模块在大学生物和化学信息学教学中的应用

白启峰1,*(),张洋3,靳玲玲1,姚小军2,4   

  1. 1 兰州大学基础医学院, 兰州 730000
    2 兰州大学化学化工学院, 兰州 730000
    3 兰州大学网络安全与信息化办公室, 兰州 730000
    4 澳门科技大学中药质量研究国家重点实验室, 澳门 999078
  • 收稿日期:2018-01-15 发布日期:2018-05-18
  • 通讯作者: 白启峰 E-mail:qifengbai@yeah.net
  • 基金资助:
    国家自然科学基金青年项目(21605066);兰州大学中央高校基本科研业务费专项资金(lzujbky-2017-122);CERNET InnovationProject(NGII20160513)

Applying Virtual Drug Screening Workflow Module of Schrödinger into College Bioinformatics and Chemoinformatics Teaching

Qifeng BAI1,*(),Yang ZHANG3,Lingling JIN1,Xiaojun YAO2,4   

  1. 1 School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, P. R. China
    2 College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China
    3 Office of Cybersecurity and Information, Lanzhou University, Lanzhou 730000, P. R. China
    4 State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, P. R. China
  • Received:2018-01-15 Published:2018-05-18
  • Contact: Qifeng BAI E-mail:qifengbai@yeah.net
  • Supported by:
    国家自然科学基金青年项目(21605066);兰州大学中央高校基本科研业务费专项资金(lzujbky-2017-122);CERNET InnovationProject(NGII20160513)

摘要:

介绍了Schrödinger药物虚拟筛选的基本原理和流程,结合大学生物和化学信息学课程的相关教学内容,分别描述了蛋白受体的预处理、类药性五原则、毒药物动力学(ADME)、泛筛选干扰化合物(PAINS)、高通量虚拟筛选、标准精度筛选、高精度筛选和MM/GBSA的打分排序原理和使用方法。该软件可以在大学生物和化学信息学的教学中演示,有助于提高学生对蛋白结构、分子构象、药物虚拟筛选和计算机辅助分子设计的理解,该软件有很好的图形界面,可以给学生直观的体验,大大丰富了大学课堂的教学内容。此外,该软件在药物设计领域里面也有很好的应用价值,大大节约了药物筛选的成本,提高了药物发现的效率。

关键词: Schrödinger, Glide, 虚拟筛选, 分子对接

Abstract:

This paper introduces the basic principle and workflow of virtual screening of drugs in Schrödinger. In combination with the college bioinformatics and chemoinformatics course, it illustrates the principle and usage method of protein preparation, Lipinski's Rule of Five, ADME, Pan-assay Interference Compounds (PAINS), high throughput virtual screening, standard precision screening, extra precision screening and score ranking of MM/GBSA. The Schrödinger can be demonstrated to improve students' understanding of protein structure, molecular conformation, virtual drug screening and computer-aided molecular design in the college bioinformatics and chemoinformatics teaching. Due to the friendly graphical interface, Schrödinger can give students the intuitive experience and enrich the college course. In addition, Schrödinger has a good application value in the drug design field. It can reduce the cost of drug screening and improve the efficiency of drug discovery.

Key words: Schrödinger, Glide, Virtual screening, Molecular docking

MSC2000: 

  • G64