Ligand docking and binding site analysis with pymol and autodock/vina
Ligand docking and binding site analysis with pymol and autodock/vina
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DOI：
10.14419/ijbas.v4i2.4123
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发表时间：
2015-03
期刊：
影响因子：
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通讯作者：
M. A. Rauf;S. Zubair;A. Azhar
中科院分区：
文献类型：
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作者：
M. A. Rauf;S. Zubair;A. Azhar
各种治疗上重要的化学实体与特定靶位点的对接提供了一种有意义的策略，其在药物设计过程中可能具有巨大的范围。为了彻底了解决定配体与其受体之间键合强度的结构特征，必须深入了解结合几何形状和相互作用。生物信息学和图形软件“PyMOL”与分子对接套件Autodock和维纳相结合，可以对分子组合进行研究，以可视化和理解基于结构的药物设计工作。在本研究中，我们概述了一个用户友好的方法来进行分子对接，最后的结果进行了分析，在两个以及三维取向的pymol。该操作绕过了使用cygwin终端进行对接所涉及的步骤，例如形成gpf和dpf文件。AutoDock 4.2程序操作简单、直观，不需要经过正式的生物信息学培训即可理解分子对接研究。
Docking of various therapeutically important chemical entities to the specific target sites offers a meaningful strategy that may have tremendous scope in a drug design process. For a thorough understanding of the structural features that determine the strength of bonding between a ligand with its receptor, an insight to visualize binding geometries and interaction is mandatory. Bioinformatical as well as graphical software ‘PyMOL’ in combination with the molecular docking suites Autodock and Vina allows the study of molecular combination to visualize and understand the structure-based drug design efforts. In the present study, we outlined a user friendly method to perform molecular docking using vina and finally the results were analyzed in pymol in both two as well as three-dimensional orientation. The operation bypasses the steps that are involved in docking using cygwin terminal like formation of gpf and dpf files. The simple and straight-forward operation method does not require formal bioinformatics training to apprehend molecular docking studies using AutoDock 4.2 program.