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首页> 外文期刊>International Journal of Basic and Applied Sciences >Ligand docking and binding site analysis with pymol and autodock/vina
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Ligand docking and binding site analysis with pymol and autodock/vina

机译：pymol和autodock / vina的配体对接和结合位点分析

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摘要

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.
机译：将各种具有治疗意义的重要化学实体对接至特定的靶位点可提供一种有意义的策略，该策略可能在药物设计过程中具有巨大的范围。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，必须可视化结合几何形状和相互作用。生物信息学以及图形化软件“ PyMOL”与分子对接套件Autodock和Vina结合使用，可以对分子组合进行研究，以可视化并了解基于结构的药物设计工作。在本研究中，我们概述了一种使用vina进行分子对接的用户友好方法，最后在pymol中以二维和三维方向对结果进行了分析。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。简单而直接的操作方法不需要正式的生物信息学培训即可了解使用AutoDock 4.2程序进行的分子对接研究。

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